[med-svn] samtools 01/01: samtools (1.1-1) unstable; urgency=medium
Charles Plessy
plessy at moszumanska.debian.org
Tue Sep 30 22:40:04 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch debian/logs/unstable
in repository samtools.
commit 08ffba18ce04fccae850160f524891f2aef04cde
Author: Charles Plessy <plessy at debian.org>
Date: Wed Oct 1 07:37:55 2014 +0900
samtools (1.1-1) unstable; urgency=medium
c448d48 Merge tag '1.1' into debian/unstable
d12ab1e Merge branch 'develop' into debian/unstable to solve issue
with regression tests needing a pseudo-terminal.
See https://github.com/samtools/samtools/issues/300
c87f8ce Add autopkg tests.
7c50b7b Removed python-wrong-path-for-interpreter.patch
(issue solved upstream).
-- Charles Plessy <plessy at debian.org> Thu, 25 Sep 2014 09:04:20 +0900
---
amd64.changes | 104 +--
arm64.log | 550 +++++++++++
armel.log | 605 ------------
dsc | 67 +-
i386.log | 2615 +++++++++++++++++++++++++++++++++++----------------
info | 21 +-
kfreebsd-amd64.log | 2234 +++++++++++++++++++++++++++++---------------
kfreebsd-i386.log | 2613 +++++++++++++++++++++++++++++++++++----------------
mipsel.log | 2624 ++++++++++++++++++++++++++++++++++++----------------
ppc64el.log | 546 +++++++++++
upload | 14 +-
11 files changed, 8134 insertions(+), 3859 deletions(-)
diff --git a/amd64.changes b/amd64.changes
index aa894c6..ee4b1f4 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -1,68 +1,62 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
+Date: Thu, 25 Sep 2014 09:04:20 +0900
Source: samtools
-Binary: samtools libbam-dev
-Architecture: source amd64
-Version: 0.1.19-1
+Binary: samtools samtools-test
+Architecture: source amd64 all
+Version: 1.1-1
Distribution: unstable
-Urgency: low
+Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
+Description:
samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
+ samtools-test - test files for the samtools package.
+Changes:
+ samtools (1.1-1) unstable; urgency=medium
.
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
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- 3a5880dd0940e98447caa70799b76a39091d3b38 557812 samtools_0.1.19.orig.tar.gz
- 4e18f7699ba4c4cf5ac9503b3bab1f017731414b 10215 samtools_0.1.19-1.debian.tar.gz
- d65798025fa3a03cc2366e0b6bf75a6fc35d48a4 562956 samtools_0.1.19-1_amd64.deb
- 8c400aca23a6ca41b36e6884665939abfd8f9352 123276 libbam-dev_0.1.19-1_amd64.deb
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- f1da7fbdc6956b7aa68dd9cad7435f1ccdc6f6601309761f3845e3a1327da77e 123276 libbam-dev_0.1.19-1_amd64.deb
-Files:
- c239aee949f239c0cb7c9329039eb827 2078 science optional samtools_0.1.19-1.dsc
- 1229dc88487a49b03e69a5c0aa2f8a1e 557812 science optional samtools_0.1.19.orig.tar.gz
- 467846afb2de05547f0ffed136290f8d 10215 science optional samtools_0.1.19-1.debian.tar.gz
- 5195be37dd92ae9c7f2657eacdd40ba2 562956 science optional samtools_0.1.19-1_amd64.deb
- 20ba2fee341db9e3659bce6165aa6763 123276 libdevel optional libbam-dev_0.1.19-1_amd64.deb
+ c448d48 Merge tag '1.1' into debian/unstable
+ d12ab1e Merge branch 'develop' into debian/unstable to solve issue
+ with regression tests needing a pseudo-terminal.
+ See https://github.com/samtools/samtools/issues/300
+ c87f8ce Add autopkg tests.
+ 7c50b7b Removed python-wrong-path-for-interpreter.patch
+ (issue solved upstream).
+Checksums-Sha1:
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+ 0e4de8be00fb4dd375048b1b1dc05e2f120e2ead 10164 samtools_1.1-1.debian.tar.xz
+ 3424183e6577c856a09f4f838c1a398c8e5744ba 378168 samtools_1.1-1_amd64.deb
+ f2542cc1d07aef31d216d43630c87c9edf38cabd 2644466 samtools-test_1.1-1_all.deb
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+ 5fb20f9d61452c8863e6ff42d2ea0d9ec72211fb9dd43cca3b55eeeb49985196 2644466 samtools-test_1.1-1_all.deb
+Files:
+ 1d7d68a126fe90d8366eb3fed809230c 378168 science optional samtools_1.1-1_amd64.deb
+ 9ffe69f7310c265243d2fd553c322435 2644466 science optional samtools-test_1.1-1_all.deb
+ 148939471e917dfe65acde2ec02d10e0 2104 science optional samtools_1.1-1.dsc
+ 5fda5c175d04bff39c56078aea7cd3b1 4320951 science optional samtools_1.1.orig.tar.gz
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diff --git a/arm64.log b/arm64.log
new file mode 100644
index 0000000..2a47d85
--- /dev/null
+++ b/arm64.log
@@ -0,0 +1,550 @@
+From buildd at arm-arm-02.debian.org Thu Sep 25 05:29:23 2014
+Return-path: <buildd at arm-arm-02.debian.org>
+Received: from muffat.debian.org ([2607:f8f0:610:4000:6564:a62:ce0c:1392])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
+ by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at arm-arm-02.debian.org>)
+ id 1XX1cI-0004X5-PQ
+ for logs at buildd.debian.org; Thu, 25 Sep 2014 05:29:22 +0000
+Received: from alwyn.islands.arm.com ([217.140.96.59]
+ helo=arm-arm-02.debian.org)
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+ CN=arm-arm-02.debian.org, EMAIL=hostmaster at arm-arm-02.debian.org (verified)
+ by muffat.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at arm-arm-02.debian.org>)
+ id 1XX1cF-0005Go-4K
+ for logs at buildd.debian.org; Thu, 25 Sep 2014 05:29:20 +0000
+Received: from buildd by arm-arm-02.debian.org with local (Exim 4.80)
+ (envelope-from <buildd at arm-arm-02.debian.org>)
+ id 1XX1cA-0004Rk-Hr; Thu, 25 Sep 2014 05:29:14 +0000
+Content-Transfer-Encoding: binary
+MIME-Version: 1.0
+X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
+Date: Thu, 25 Sep 2014 05:29:14 +0000
+From: buildd on arm-arm-02 <buildd at arm-arm-02.debian.org>
+To: buildd-porters at arm-arm-02.debian.org,
+ logs at buildd.debian.org
+Subject: Log for attempted build of samtools_1.1-1 on arm64 (dist=sid)
+Key-Id: 9EA3BEB5
+Message-Id: <E1XX1cA-0004Rk-Hr at arm-arm-02.debian.org>
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.64.0 (17 May 2013) on arm-arm-02.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 1.1-1 (arm64) 25 Sep 2014 00:25 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 1.1-1
+Source Version: 1.1-1
+Distribution: sid
+Machine Architecture: armhf
+Host Architecture: arm64
+Build Architecture: arm64
+
+I: NOTICE: Log filtering will replace 'build/samtools-AekwtD/samtools-1.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-AekwtD' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-arm64-sbuild-871154a1-ba07-424d-b1df-148f48b013a7' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://ftp.debian.org unstable InRelease [233 kB]
+Get:2 http://ftp.uk.debian.org unstable InRelease [233 kB]
+Get:3 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:4 http://ftp.debian.org unstable/main Sources [7548 kB]
+Get:5 http://ftp.uk.debian.org unstable/main Sources [7548 kB]
+Get:6 http://incoming.debian.org buildd-unstable/main Sources [358 kB]
+Get:7 http://incoming.debian.org buildd-unstable/contrib Sources [1136 B]
+Get:8 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
+Get:9 http://incoming.debian.org buildd-unstable/main arm64 Packages [332 kB]
+Get:10 http://incoming.debian.org buildd-unstable/contrib arm64 Packages [844 B]
+Get:11 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
+Get:12 http://ftp.debian.org unstable/non-free Sources [107 kB]
+Get:13 http://ftp.debian.org unstable/main arm64 Packages [5808 kB]
+Get:14 http://ftp.debian.org unstable/contrib arm64 Packages [28.4 kB]
+Get:15 http://ftp.uk.debian.org unstable/contrib Sources [57.1 kB]
+Get:16 http://ftp.uk.debian.org unstable/non-free Sources [107 kB]
+Get:17 http://ftp.uk.debian.org unstable/main arm64 Packages [5808 kB]
+Get:18 http://ftp.uk.debian.org unstable/contrib arm64 Packages [28.4 kB]
+Fetched 28.4 MB in 39s (711 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 4333 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
+Fetched 4333 kB in 2s (1724 kB/s)
+Download complete and in download only mode
+
+Check arch
+──────────
+
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-0BR0BW/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
+Need to get 0 B/820 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ... 11543 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-aJizjS/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf tabix zlib1g-dev
+Suggested packages:
+ wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
+ www-browser libmail-box-perl
+Recommended packages:
+ curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
+ libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ libmail-sendmail-perl
+The following NEW packages will be installed:
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
+ zlib1g-dev
+0 upgraded, 25 newly installed, 0 to remove and 3 not upgraded.
+Need to get 9547 kB/9548 kB of archives.
+After this operation, 29.2 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 arm64 1.3.1-1 [23.6 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base arm64 1.22.2-8 [1141 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils arm64 9.0.5+b3 [178 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db arm64 2.7.0.1-1 [973 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 arm64 0.19.2-2+b1 [30.9 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 arm64 1:5.19-2 [231 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 arm64 2.9.1+dfsg1-4+b2 [692 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libffi6 arm64 3.1-2+b2 [18.9 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 arm64 2.42.0-1 [2295 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 arm64 0.6.8-3 [119 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libhts1 arm64 1.1-1 [171 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 arm64 0.9.3-5.2+b2 [257 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main file arm64 1:5.19-2 [58.2 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext-base arm64 0.19.2-2+b1 [118 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext arm64 0.19.2-2+b1 [1175 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main libhts-dev arm64 1.1-1 [225 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev arm64 5.9+20140913-1+b1 [71.7 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev arm64 5.9+20140913-1+b1 [163 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main tabix arm64 1.1-1 [160 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev arm64 1:1.2.8.dfsg-2 [200 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 9547 kB in 44s (216 kB/s)
+Selecting previously unselected package libpipeline1:arm64.
+(Reading database ... 11543 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.3.1-1_arm64.deb ...
+Unpacking libpipeline1:arm64 (1.3.1-1) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.2-8_arm64.deb ...
+Unpacking groff-base (1.22.2-8) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.5+b3_arm64.deb ...
+Unpacking bsdmainutils (9.0.5+b3) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.0.1-1_arm64.deb ...
+Unpacking man-db (2.7.0.1-1) ...
+Selecting previously unselected package bash-completion.
+Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
+Unpacking bash-completion (1:2.1-4) ...
+Selecting previously unselected package libasprintf0c2:arm64.
+Preparing to unpack .../libasprintf0c2_0.19.2-2+b1_arm64.deb ...
+Unpacking libasprintf0c2:arm64 (0.19.2-2+b1) ...
+Selecting previously unselected package libmagic1:arm64.
+Preparing to unpack .../libmagic1_1%3a5.19-2_arm64.deb ...
+Unpacking libmagic1:arm64 (1:5.19-2) ...
+Selecting previously unselected package libxml2:arm64.
+Preparing to unpack .../libxml2_2.9.1+dfsg1-4+b2_arm64.deb ...
+Unpacking libxml2:arm64 (2.9.1+dfsg1-4+b2) ...
+Selecting previously unselected package libffi6:arm64.
+Preparing to unpack .../libffi6_3.1-2+b2_arm64.deb ...
+Unpacking libffi6:arm64 (3.1-2+b2) ...
+Selecting previously unselected package libglib2.0-0:arm64.
+Preparing to unpack .../libglib2.0-0_2.42.0-1_arm64.deb ...
+Unpacking libglib2.0-0:arm64 (2.42.0-1) ...
+Selecting previously unselected package libcroco3:arm64.
+Preparing to unpack .../libcroco3_0.6.8-3_arm64.deb ...
+Unpacking libcroco3:arm64 (0.6.8-3) ...
+Selecting previously unselected package libhts1:arm64.
+Preparing to unpack .../libhts1_1.1-1_arm64.deb ...
+Unpacking libhts1:arm64 (1.1-1) ...
+Selecting previously unselected package libunistring0:arm64.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b2_arm64.deb ...
+Unpacking libunistring0:arm64 (0.9.3-5.2+b2) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.19-2_arm64.deb ...
+Unpacking file (1:5.19-2) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.2-2+b1_arm64.deb ...
+Unpacking gettext-base (0.19.2-2+b1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.2-2+b1_arm64.deb ...
+Unpacking gettext (0.19.2-2+b1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.1) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
+Unpacking po-debconf (1.0.16+nmu3) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20140817_all.deb ...
+Unpacking debhelper (9.20140817) ...
+Selecting previously unselected package libhts-dev:arm64.
+Preparing to unpack .../libhts-dev_1.1-1_arm64.deb ...
+Unpacking libhts-dev:arm64 (1.1-1) ...
+Selecting previously unselected package libtinfo-dev:arm64.
+Preparing to unpack .../libtinfo-dev_5.9+20140913-1+b1_arm64.deb ...
+Unpacking libtinfo-dev:arm64 (5.9+20140913-1+b1) ...
+Selecting previously unselected package libncurses5-dev:arm64.
+Preparing to unpack .../libncurses5-dev_5.9+20140913-1+b1_arm64.deb ...
+Unpacking libncurses5-dev:arm64 (5.9+20140913-1+b1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../archives/tabix_1.1-1_arm64.deb ...
+Unpacking tabix (1.1-1) ...
+Selecting previously unselected package zlib1g-dev:arm64.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_arm64.deb ...
+Unpacking zlib1g-dev:arm64 (1:1.2.8.dfsg-2) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up libpipeline1:arm64 (1.3.1-1) ...
+Setting up groff-base (1.22.2-8) ...
+Setting up bsdmainutils (9.0.5+b3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up man-db (2.7.0.1-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up bash-completion (1:2.1-4) ...
+Setting up libasprintf0c2:arm64 (0.19.2-2+b1) ...
+Setting up libmagic1:arm64 (1:5.19-2) ...
+Setting up libxml2:arm64 (2.9.1+dfsg1-4+b2) ...
+Setting up libffi6:arm64 (3.1-2+b2) ...
+Setting up libglib2.0-0:arm64 (2.42.0-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:arm64 (0.6.8-3) ...
+Setting up libhts1:arm64 (1.1-1) ...
+Setting up libunistring0:arm64 (0.9.3-5.2+b2) ...
+Setting up file (1:5.19-2) ...
+Setting up gettext-base (0.19.2-2+b1) ...
+Setting up gettext (0.19.2-2+b1) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu3) ...
+Setting up debhelper (9.20140817) ...
+Setting up libhts-dev:arm64 (1.1-1) ...
+Setting up libtinfo-dev:arm64 (5.9+20140913-1+b1) ...
+Setting up libncurses5-dev:arm64 (5.9+20140913-1+b1) ...
+Setting up tabix (1.1-1) ...
+Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-11) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 3.16.0 armhf (aarch64)
+Toolchain package versions: binutils_2.24.51.20140918-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-15 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 linux-libc-dev_3.16.3-2
+Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.1 base-files_7.5+b2 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140918-1 bsdmainutils_9.0.5+b3 bsdutils_1:2.20.1-5.8+b2 build-essential_11.7 bzip2_1.0.6-7+b2 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-15 dash_0.5.7-4+b2 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4+b2 diffutils_1:3.3-1+b2 dmsetup_2:1.02.90-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_ [...]
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.1
+dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
+dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying dynamic-build.patch
+dpkg-source: info: applying debian-changes
+
+Check disc space
+────────────────
+
+Sufficient free space for build
+
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=parallel=6
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=sid-arm64-sbuild
+SCHROOT_CHROOT_NAME=sid-arm64-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-arm64-sbuild-871154a1-ba07-424d-b1df-148f48b013a7
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.1
+dpkg-buildpackage: host architecture arm64
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+ fakeroot debian/rules clean
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j6 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f TAGS
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_auto_configure -a -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j6 HTSDIR=/usr/include HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lcurs [...]
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j6 test HTSDIR=/usr/include HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+make[2]: Entering directory '/«PKGBUILDDIR»'
+REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/PMW4HD3gTH/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/PMW4HD3gTH/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/PMW4HD3gTH/bgzip.dat.gz
+.. ok
+
+Signal caught, cleaning and exiting...
+make[1]: *** [override_dh_auto_test] Terminated
+make[2]: *** wait: No child processes. Stop.
+make[2]: *** Waiting for unfinished jobs....
+make[2]: *** wait: No child processes. Stop.
+E: Caught signal ‘Terminated’: terminating immediately
+make: *** [build-arch] Terminated
+debian/rules:18: recipe for target 'override_dh_auto_test' failed
+debian/rules:6: recipe for target 'build-arch' failed
+The command failed [15]: /«PKGBUILDDIR»/samtools faidx /tmp/PMW4HD3gTH/faidx.fa
+out:
+err:
+ at test/test.pl line 67.
+ main::error("The command failed [15]: /«PKGBUILDDIR»/"..., "out:\x{a}", "err:\x{a}") called at test/test.pl line 138
+ main::cmd("/«PKGBUILDDIR»/samtools faidx /tmp/PMW4H"...) called at test/test.pl line 390
+ main::test_faidx(HASH(0x13b5fec8)) called at test/test.pl line 36
+Build killed with signal TERM after 300 minutes of inactivity
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20140925-0529
+
+Finished
+────────
+
+E: Build failure (dpkg-buildpackage died)
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build Architecture: arm64
+Build-Space: 23848
+Build-Time: 18043
+Distribution: sid
+Fail-Stage: build
+Host Architecture: arm64
+Install-Time: 93
+Job: samtools_1.1-1
+Machine Architecture: armhf
+Package: samtools
+Package-Time: 18199
+Source-Version: 1.1-1
+Space: 23848
+Status: attempted
+Version: 1.1-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20140925-0529
+Build needed 05:03:19, 23848k disc space
diff --git a/armel.log b/armel.log
index 6d3e382..e69de29 100644
--- a/armel.log
+++ b/armel.log
@@ -1,605 +0,0 @@
-From buildd at alwyn.debian.org Sat Mar 30 09:39:54 2013
-Return-path: <buildd at alwyn.debian.org>
-Received: from mailly.debian.org ([82.195.75.114])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at alwyn.debian.org>)
- id 1ULsGQ-0006To-8J
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:39:54 +0000
-Received: from alwyn.islands.arm.com ([217.140.96.59] helo=alwyn.debian.org)
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=alwyn.debian.org, EMAIL=hostmaster at alwyn.debian.org (verified)
- by mailly.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
- (Exim 4.80) (envelope-from <buildd at alwyn.debian.org>)
- id 1ULsGP-0004Ob-4I
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:39:53 +0000
-Received: from buildd by alwyn.debian.org with local (Exim 4.72)
- (envelope-from <buildd at alwyn.debian.org>)
- id 1ULsGO-0003bY-7L; Sat, 30 Mar 2013 09:39:52 +0000
-Date: Sat, 30 Mar 2013 09:39:52 +0000
-Message-Id: <E1ULsGO-0003bY-7L at alwyn.debian.org>
-From: buildd on alwyn <buildd at alwyn.debian.org>
-To: buildd-porters at alwyn.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.19-1 on armel (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alwyn.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (armel) 30 Mar 2013 09:29 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: armel
-Get:1 http://ftp.uk.debian.org unstable InRelease [236 kB]
-Get:2 http://incoming.debian.org unstable InRelease [236 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [6484 kB]
-Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:5 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [51.0 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armel Packages [6113 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://incoming.debian.org unstable/main armel Packages [6113 kB]
-Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [35.7 kB]
-Get:13 http://incoming.debian.org unstable/contrib armel Packages [35.7 kB]
-Get:14 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:15 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:16 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:17 http://incoming.debian.org buildd-unstable/main armel Packages [13.1 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib armel Packages [14 B]
-Fetched 26.2 MB in 1min 43s (253 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (399 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 63 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 63 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (6.12)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
-coreutils: already installed (8.13-3.3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-7)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.12-2)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-15)
-sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-32)
-sysvinit: already installed (2.88dsf-32)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.2)
-mount: already installed (2.20.1-5.2)
-util-linux: already installed (2.20.1-5.2)
-libc6-dev: already installed (2.13-36)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 63 not upgraded.
-Need to get 9834 kB of archives.
-After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.2-2 [35.4 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.22.2-1 [674 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.4 [212 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.3-3 [868 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armel 0.18.1.1-10 [26.6 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 1:5.11-2.1 [200 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 1:8.31-2 [246 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.8.0+dfsg1-7+nmu1 [825 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armel 3.0.10-3 [22.8 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.33.12+really2.32.4-5 [1694 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.6-2 [120 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armel 0.18.1.1-10 [132 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main file armel 1:5.11-2.1 [51.5 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-10 [138 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libasprintf-dev armel 0.18.1.1-10 [26.5 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo-dev armel 0.18.1.1-10 [163 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-10 [1749 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.55-3 [28.6 kB]
-Get:26 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armel 5.9-10 [90.3 kB]
-Get:27 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-10 [205 kB]
-Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.7.dfsg-13 [211 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9834 kB in 5s (1841 kB/s)
-Selecting previously unselected package libpipeline1:armel.
-(Reading database ... 10693 files and directories currently installed.)
-Unpacking libpipeline1:armel (from .../libpipeline1_1.2.2-2_armel.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_armel.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_armel.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_armel.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:armel.
-Unpacking libasprintf0c2:armel (from .../libasprintf0c2_0.18.1.1-10_armel.deb) ...
-Selecting previously unselected package libmagic1:armel.
-Unpacking libmagic1:armel (from .../libmagic1_1%3a5.11-2.1_armel.deb) ...
-Selecting previously unselected package libpcre3:armel.
-Unpacking libpcre3:armel (from .../libpcre3_1%3a8.31-2_armel.deb) ...
-Selecting previously unselected package libxml2:armel.
-Unpacking libxml2:armel (from .../libxml2_2.8.0+dfsg1-7+nmu1_armel.deb) ...
-Selecting previously unselected package libffi5:armel.
-Unpacking libffi5:armel (from .../libffi5_3.0.10-3_armel.deb) ...
-Selecting previously unselected package libglib2.0-0:armel.
-Unpacking libglib2.0-0:armel (from .../libglib2.0-0_2.33.12+really2.32.4-5_armel.deb) ...
-Selecting previously unselected package libcroco3:armel.
-Unpacking libcroco3:armel (from .../libcroco3_0.6.6-2_armel.deb) ...
-Selecting previously unselected package libunistring0:armel.
-Unpacking libunistring0:armel (from .../libunistring0_0.9.3-5_armel.deb) ...
-Selecting previously unselected package libgettextpo0:armel.
-Unpacking libgettextpo0:armel (from .../libgettextpo0_0.18.1.1-10_armel.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_armel.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_armel.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
-Selecting previously unselected package libasprintf-dev:armel.
-Unpacking libasprintf-dev:armel (from .../libasprintf-dev_0.18.1.1-10_armel.deb) ...
-Selecting previously unselected package libgettextpo-dev:armel.
-Unpacking libgettextpo-dev:armel (from .../libgettextpo-dev_0.18.1.1-10_armel.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_armel.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_armel.deb) ...
-Selecting previously unselected package libtinfo-dev:armel.
-Unpacking libtinfo-dev:armel (from .../libtinfo-dev_5.9-10_armel.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_armel.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:armel.
-Unpacking zlib1g-dev:armel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_armel.deb) ...
-Setting up libpipeline1:armel (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:armel (0.18.1.1-10) ...
-Setting up libmagic1:armel (1:5.11-2.1) ...
-Setting up libpcre3:armel (1:8.31-2) ...
-Setting up libxml2:armel (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:armel (3.0.10-3) ...
-Setting up libglib2.0-0:armel (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:armel (0.6.6-2) ...
-Setting up libunistring0:armel (0.9.3-5) ...
-Setting up libgettextpo0:armel (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:armel (0.18.1.1-10) ...
-Setting up libgettextpo-dev:armel (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:armel (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:armel (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 63 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 fil [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture armel
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-Line 2, sequence length 35 vs 8960 from CIGAR
-Parse error at line 2: CIGAR and sequence length are inconsistent
-make[1]: *** [ex1.bam] Aborted
-make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/examples'
-make: *** [debian/stamp-makefile-check] Error 2
-dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0939
-FAILED [dpkg-buildpackage died]
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-34e2c03c-0d4b-40b8-90e6-24a2760cc633/build/buildd-samtools_0.1.19-1-armel-DBqlzN
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: armel
-Build-Space: 7864
-Build-Time: 341
-Distribution: sid
-Fail-Stage: build
-Install-Time: 110
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 590
-Source-Version: 0.1.19-1
-Space: 7864
-Status: attempted
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0939
-Build needed 00:09:50, 7864k disc space
-
diff --git a/dsc b/dsc
index 7adef0c..a993eb4 100644
--- a/dsc
+++ b/dsc
@@ -1,45 +1,46 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
Format: 3.0 (quilt)
Source: samtools
-Binary: samtools, libbam-dev
-Architecture: any
-Version: 0.1.19-1
+Binary: samtools, samtools-test
+Architecture: any all
+Version: 1.1-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>, Dominique Belhachemi <domibel at debian.org>
-Homepage: http://samtools.sourceforge.net
-Standards-Version: 3.9.4
+Homepage: http://www.htslib.org/
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/samtools.git
Vcs-Git: git://anonscm.debian.org/debian-med/samtools.git
-Build-Depends: debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Package-List:
- libbam-dev deb libdevel optional
- samtools deb science optional
-Checksums-Sha1:
- 3a5880dd0940e98447caa70799b76a39091d3b38 557812 samtools_0.1.19.orig.tar.gz
- 4e18f7699ba4c4cf5ac9503b3bab1f017731414b 10215 samtools_0.1.19-1.debian.tar.gz
-Checksums-Sha256:
- 180c120a040ec660ebecc30ebae664772c0fd503e028173ab2496379bc208c17 557812 samtools_0.1.19.orig.tar.gz
- 980683591cb084f5f825baeffb3c7f08acf01a1a13b8f41e3770b3ee731190a3 10215 samtools_0.1.19-1.debian.tar.gz
-Files:
- 1229dc88487a49b03e69a5c0aa2f8a1e 557812 samtools_0.1.19.orig.tar.gz
- 467846afb2de05547f0ffed136290f8d 10215 samtools_0.1.19-1.debian.tar.gz
+Testsuite: autopkgtest
+Build-Depends: debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+Package-List:
+ samtools deb science optional arch=any
+ samtools-test deb science optional arch=all
+Checksums-Sha1:
+ ca446ec24eabd2f71605dde55a787f182cb50f13 4320951 samtools_1.1.orig.tar.gz
+ 0e4de8be00fb4dd375048b1b1dc05e2f120e2ead 10164 samtools_1.1-1.debian.tar.xz
+Checksums-Sha256:
+ cee231e33b7290be8e07dea43a99b885d9df79d957625ac84879b47ff91cda69 4320951 samtools_1.1.orig.tar.gz
+ 50e5d2299c2d99ce53647fc0cb08eee53bc31d08bfa7d7cc981e6fae28ab231b 10164 samtools_1.1-1.debian.tar.xz
+Files:
+ 5fda5c175d04bff39c56078aea7cd3b1 4320951 samtools_1.1.orig.tar.gz
+ 40b3a1f31e22323c8d247e1bff1a9c52 10164 samtools_1.1-1.debian.tar.xz
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diff --git a/i386.log b/i386.log
index 7e6e73c..626d5f2 100644
--- a/i386.log
+++ b/i386.log
@@ -1,65 +1,74 @@
-From buildd at biber.debian.org Sat Mar 30 09:18:53 2013
-Return-path: <buildd at biber.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1ULrw4-0002p3-U6
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:18:53 +0000
-Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1ULrw3-0001as-KD; Sat, 30 Mar 2013 09:18:51 +0000
-Received: from buildd by biber.debian.org with local (Exim 4.72)
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- id 1ULrw2-0001be-CE; Sat, 30 Mar 2013 09:18:50 +0000
-Message-Id: <E1ULrw2-0001be-CE at biber.debian.org>
-MIME-Version: 1.0
+From buildd at brahms.debian.org Thu Sep 25 00:27:27 2014
+Return-path: <buildd at brahms.debian.org>
+Received: from mailly.debian.org ([2001:41b8:202:deb:6564:a62:52c3:4b72])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
+ by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at brahms.debian.org>)
+ id 1XWwu7-0007j9-7F
+ for logs at buildd.debian.org; Thu, 25 Sep 2014 00:27:27 +0000
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+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=brahms.debian.org, EMAIL=hostmaster at brahms.debian.org (verified)
+ by mailly.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at brahms.debian.org>)
+ id 1XWwu6-0004pk-By
+ for logs at buildd.debian.org; Thu, 25 Sep 2014 00:27:26 +0000
+Received: from buildd by brahms.debian.org with local (Exim 4.80)
+ (envelope-from <buildd at brahms.debian.org>)
+ id 1XWwu4-0005ih-Eq; Thu, 25 Sep 2014 00:27:24 +0000
Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 30 Mar 2013 09:18:50 +0000
-From: buildd on biber <buildd at biber.debian.org>
-To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on i386 (dist=sid)
-Key-Id: DFABA12A
+MIME-Version: 1.0
+X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
+Date: Thu, 25 Sep 2014 00:27:24 +0000
+From: buildd on brahms <buildd at brahms.debian.org>
+To: buildd-admin at brahms.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_1.1-1 on i386 (dist=sid)
+Key-Id: 4C7A7FBE
+Message-Id: <E1XWwu4-0005ih-Eq at brahms.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
+sbuild (Debian sbuild) 0.64.0 (17 May 2013) on brahms.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (i386) 30 Mar 2013 09:16 ║
+║ samtools 1.1-1 (i386) 25 Sep 2014 00:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable Release.gpg [836 B]
-Get:2 http://ftp.gr.debian.org unstable Release [235 kB]
-Get:3 http://ftp.gr.debian.org unstable/main Sources [6484 kB]
-Get:4 http://incoming.debian.org unstable Release.gpg [836 B]
-Get:5 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
-Get:6 http://ftp.gr.debian.org unstable/contrib Sources [51.0 kB]
-Get:7 http://ftp.gr.debian.org unstable/non-free Sources [101 kB]
-Get:8 http://ftp.gr.debian.org unstable/main i386 Packages [6278 kB]
-Get:9 http://incoming.debian.org unstable Release [235 kB]
-Get:10 http://ftp.gr.debian.org unstable/contrib i386 Packages [44.5 kB]
-Get:11 http://incoming.debian.org buildd-unstable Release [109 kB]
-Get:12 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:15 http://incoming.debian.org unstable/main i386 Packages [6278 kB]
-Get:16 http://incoming.debian.org unstable/contrib i386 Packages [44.5 kB]
-Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:20 http://incoming.debian.org buildd-unstable/main i386 Packages [14.2 kB]
-Get:21 http://incoming.debian.org buildd-unstable/contrib i386 Packages [436 B]
-Fetched 26.5 MB in 18s (1443 kB/s)
+Version: 1.1-1
+Source Version: 1.1-1
+Distribution: sid
+Machine Architecture: amd64
+Host Architecture: i386
+Build Architecture: i386
+
+I: NOTICE: Log filtering will replace 'build/samtools-YjmHXD/samtools-1.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-YjmHXD' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-i386-sbuild-813c0d07-75a0-43f9-aa37-749f9218ed0c' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://mirror-ubc.debian.org unstable InRelease [233 kB]
+Get:2 http://mirror-ubc.debian.org unstable/main Sources [7548 kB]
+Get:3 http://ftp.debian.org unstable InRelease [233 kB]
+Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [57.1 kB]
+Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [107 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main i386 Packages [6986 kB]
+Get:8 http://incoming.debian.org buildd-unstable/main Sources [358 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib i386 Packages [53.1 kB]
+Get:10 http://ftp.debian.org unstable/main Sources [7548 kB]
+Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1136 B]
+Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
+Get:13 http://incoming.debian.org buildd-unstable/main i386 Packages [294 kB]
+Get:14 http://incoming.debian.org buildd-unstable/contrib i386 Packages [1364 B]
+Get:15 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
+Get:16 http://ftp.debian.org unstable/non-free Sources [107 kB]
+Get:17 http://ftp.debian.org unstable/main i386 Packages [6986 kB]
+Get:18 http://ftp.debian.org unstable/contrib i386 Packages [53.1 kB]
+Fetched 30.7 MB in 19s (1542 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,239 +89,236 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (293 kB/s)
+Need to get 4333 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
+Fetched 4333 kB in 6s (693 kB/s)
Download complete and in download only mode
Check arch
──────────
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-oiP7_X/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
+│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
+Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Removing negative dependencies:
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 29 not upgraded.
+Need to get 0 B/818 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ... 10660 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-qL3kk0/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
+│ Install samtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.13-3.3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.10)
-e2fsprogs: already installed (1.42.5-1.1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
+Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5 libncurses5-dev libpipeline1 libtinfo-dev
+ libtinfo5 libunistring0 libxml2 man-db ncurses-bin po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
+ wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
+ www-browser libmail-box-perl
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
+ libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 2 not upgraded.
-Need to get 10.2 MB of archives.
-After this operation, 29.3 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.2-2 [39.1 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.22.2-1 [736 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 9.0.4 [206 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.3-3 [890 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main libasprintf0c2 i386 0.18.1.1-10 [27.1 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 1:5.11-2.1 [204 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 1:8.31-2 [246 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.8.0+dfsg1-7+nmu1 [893 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libffi5 i386 3.0.10-3 [21.0 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.33.12+really2.32.4-5 [1829 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.6-2 [133 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main libgettextpo0 i386 0.18.1.1-10 [141 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main file i386 1:5.11-2.1 [51.6 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-10 [132 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main libasprintf-dev i386 0.18.1.1-10 [26.6 kB]
-Get:20 http://ftp.gr.debian.org/debian/ unstable/main libgettextpo-dev i386 0.18.1.1-10 [170 kB]
-Get:21 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-10 [1769 kB]
-Get:22 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.55-3 [29.3 kB]
-Get:26 http://ftp.gr.debian.org/debian/ unstable/main libtinfo-dev i386 5.9-10 [93.2 kB]
-Get:27 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-10 [212 kB]
-Get:28 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.7.dfsg-13 [212 kB]
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
+ zlib1g-dev
+The following packages will be upgraded:
+ libncurses5 libtinfo5 ncurses-bin
+3 upgraded, 25 newly installed, 0 to remove and 26 not upgraded.
+Need to get 11.0 MB/11.0 MB of archives.
+After this operation, 31.9 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin i386 5.9+20140913-1 [348 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 i386 5.9+20140913-1 [282 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 i386 5.9+20140913-1 [103 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 i386 1.3.1-1 [27.6 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main groff-base i386 1.22.2-8 [1167 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils i386 9.0.5 [207 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main man-db i386 2.7.0.1-1 [1008 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 i386 0.19.2-2 [30.9 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 i386 1:5.19-2 [242 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 i386 2.9.1+dfsg1-4 [828 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 i386 3.1-2 [17.9 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 i386 2.42.0-1 [2545 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 i386 0.6.8-3 [141 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 i386 1.1-1 [215 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5.2 [284 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file i386 1:5.19-2 [58.0 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base i386 0.19.2-2 [121 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext i386 0.19.2-2 [1243 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev i386 1.1-1 [255 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev i386 5.9+20140913-1 [76.0 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev i386 5.9+20140913-1 [177 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main tabix i386 1.1-1 [197 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.8.dfsg-2 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.2 MB in 1s (7037 kB/s)
+Fetched 11.0 MB in 1s (6462 kB/s)
+(Reading database ... 10660 files and directories currently installed.)
+Preparing to unpack .../ncurses-bin_5.9+20140913-1_i386.deb ...
+Unpacking ncurses-bin (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up ncurses-bin (5.9+20140913-1) ...
+(Reading database ... 10660 files and directories currently installed.)
+Preparing to unpack .../libtinfo5_5.9+20140913-1_i386.deb ...
+Unpacking libtinfo5:i386 (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up libtinfo5:i386 (5.9+20140913-1) ...
+Processing triggers for libc-bin (2.19-11) ...
+(Reading database ... 10660 files and directories currently installed.)
+Preparing to unpack .../libncurses5_5.9+20140913-1_i386.deb ...
+Unpacking libncurses5:i386 (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up libncurses5:i386 (5.9+20140913-1) ...
+Processing triggers for libc-bin (2.19-11) ...
Selecting previously unselected package libpipeline1:i386.
-(Reading database ... 10888 files and directories currently installed.)
-Unpacking libpipeline1:i386 (from .../libpipeline1_1.2.2-2_i386.deb) ...
+(Reading database ... 10660 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.3.1-1_i386.deb ...
+Unpacking libpipeline1:i386 (1.3.1-1) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_i386.deb) ...
+Preparing to unpack .../groff-base_1.22.2-8_i386.deb ...
+Unpacking groff-base (1.22.2-8) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_i386.deb) ...
+Preparing to unpack .../bsdmainutils_9.0.5_i386.deb ...
+Unpacking bsdmainutils (9.0.5) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_i386.deb) ...
+Preparing to unpack .../man-db_2.7.0.1-1_i386.deb ...
+Unpacking man-db (2.7.0.1-1) ...
Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
+Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
+Unpacking bash-completion (1:2.1-4) ...
Selecting previously unselected package libasprintf0c2:i386.
-Unpacking libasprintf0c2:i386 (from .../libasprintf0c2_0.18.1.1-10_i386.deb) ...
+Preparing to unpack .../libasprintf0c2_0.19.2-2_i386.deb ...
+Unpacking libasprintf0c2:i386 (0.19.2-2) ...
Selecting previously unselected package libmagic1:i386.
-Unpacking libmagic1:i386 (from .../libmagic1_1%3a5.11-2.1_i386.deb) ...
-Selecting previously unselected package libpcre3:i386.
-Unpacking libpcre3:i386 (from .../libpcre3_1%3a8.31-2_i386.deb) ...
+Preparing to unpack .../libmagic1_1%3a5.19-2_i386.deb ...
+Unpacking libmagic1:i386 (1:5.19-2) ...
Selecting previously unselected package libxml2:i386.
-Unpacking libxml2:i386 (from .../libxml2_2.8.0+dfsg1-7+nmu1_i386.deb) ...
-Selecting previously unselected package libffi5:i386.
-Unpacking libffi5:i386 (from .../libffi5_3.0.10-3_i386.deb) ...
+Preparing to unpack .../libxml2_2.9.1+dfsg1-4_i386.deb ...
+Unpacking libxml2:i386 (2.9.1+dfsg1-4) ...
+Selecting previously unselected package libffi6:i386.
+Preparing to unpack .../libffi6_3.1-2_i386.deb ...
+Unpacking libffi6:i386 (3.1-2) ...
Selecting previously unselected package libglib2.0-0:i386.
-Unpacking libglib2.0-0:i386 (from .../libglib2.0-0_2.33.12+really2.32.4-5_i386.deb) ...
+Preparing to unpack .../libglib2.0-0_2.42.0-1_i386.deb ...
+Unpacking libglib2.0-0:i386 (2.42.0-1) ...
Selecting previously unselected package libcroco3:i386.
-Unpacking libcroco3:i386 (from .../libcroco3_0.6.6-2_i386.deb) ...
+Preparing to unpack .../libcroco3_0.6.8-3_i386.deb ...
+Unpacking libcroco3:i386 (0.6.8-3) ...
+Selecting previously unselected package libhts1:i386.
+Preparing to unpack .../libhts1_1.1-1_i386.deb ...
+Unpacking libhts1:i386 (1.1-1) ...
Selecting previously unselected package libunistring0:i386.
-Unpacking libunistring0:i386 (from .../libunistring0_0.9.3-5_i386.deb) ...
-Selecting previously unselected package libgettextpo0:i386.
-Unpacking libgettextpo0:i386 (from .../libgettextpo0_0.18.1.1-10_i386.deb) ...
+Preparing to unpack .../libunistring0_0.9.3-5.2_i386.deb ...
+Unpacking libunistring0:i386 (0.9.3-5.2) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_i386.deb) ...
+Preparing to unpack .../file_1%3a5.19-2_i386.deb ...
+Unpacking file (1:5.19-2) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_i386.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
-Selecting previously unselected package libasprintf-dev:i386.
-Unpacking libasprintf-dev:i386 (from .../libasprintf-dev_0.18.1.1-10_i386.deb) ...
-Selecting previously unselected package libgettextpo-dev:i386.
-Unpacking libgettextpo-dev:i386 (from .../libgettextpo-dev_0.18.1.1-10_i386.deb) ...
+Preparing to unpack .../gettext-base_0.19.2-2_i386.deb ...
+Unpacking gettext-base (0.19.2-2) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_i386.deb) ...
+Preparing to unpack .../gettext_0.19.2-2_i386.deb ...
+Unpacking gettext (0.19.2-2) ...
Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.1) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
+Unpacking po-debconf (1.0.16+nmu3) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_i386.deb) ...
+Preparing to unpack .../debhelper_9.20140817_all.deb ...
+Unpacking debhelper (9.20140817) ...
+Selecting previously unselected package libhts-dev:i386.
+Preparing to unpack .../libhts-dev_1.1-1_i386.deb ...
+Unpacking libhts-dev:i386 (1.1-1) ...
Selecting previously unselected package libtinfo-dev:i386.
-Unpacking libtinfo-dev:i386 (from .../libtinfo-dev_5.9-10_i386.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_i386.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
+Preparing to unpack .../libtinfo-dev_5.9+20140913-1_i386.deb ...
+Unpacking libtinfo-dev:i386 (5.9+20140913-1) ...
+Selecting previously unselected package libncurses5-dev:i386.
+Preparing to unpack .../libncurses5-dev_5.9+20140913-1_i386.deb ...
+Unpacking libncurses5-dev:i386 (5.9+20140913-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../archives/tabix_1.1-1_i386.deb ...
+Unpacking tabix (1.1-1) ...
Selecting previously unselected package zlib1g-dev:i386.
-Unpacking zlib1g-dev:i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_i386.deb) ...
-Setting up libpipeline1:i386 (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_i386.deb ...
+Unpacking zlib1g-dev:i386 (1:1.2.8.dfsg-2) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up libpipeline1:i386 (1.3.1-1) ...
+Setting up groff-base (1.22.2-8) ...
+Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:i386 (0.18.1.1-10) ...
-Setting up libmagic1:i386 (1:5.11-2.1) ...
-Setting up libpcre3:i386 (1:8.31-2) ...
-Setting up libxml2:i386 (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:i386 (3.0.10-3) ...
-Setting up libglib2.0-0:i386 (2.33.12+really2.32.4-5) ...
+Setting up man-db (2.7.0.1-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up bash-completion (1:2.1-4) ...
+Setting up libasprintf0c2:i386 (0.19.2-2) ...
+Setting up libmagic1:i386 (1:5.19-2) ...
+Setting up libxml2:i386 (2.9.1+dfsg1-4) ...
+Setting up libffi6:i386 (3.1-2) ...
+Setting up libglib2.0-0:i386 (2.42.0-1) ...
No schema files found: doing nothing.
-Setting up libcroco3:i386 (0.6.6-2) ...
-Setting up libunistring0:i386 (0.9.3-5) ...
-Setting up libgettextpo0:i386 (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:i386 (0.18.1.1-10) ...
-Setting up libgettextpo-dev:i386 (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
+Setting up libcroco3:i386 (0.6.8-3) ...
+Setting up libhts1:i386 (1.1-1) ...
+Setting up libunistring0:i386 (0.9.3-5.2) ...
+Setting up file (1:5.19-2) ...
+Setting up gettext-base (0.19.2-2) ...
+Setting up gettext (0.19.2-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:i386 (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:i386 (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5 linux-libc-dev_3.2.39-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.1 [...]
+Setting up po-debconf (1.0.16+nmu3) ...
+Setting up debhelper (9.20140817) ...
+Setting up libhts-dev:i386 (1.1-1) ...
+Setting up libtinfo-dev:i386 (5.9+20140913-1) ...
+Setting up libncurses5-dev:i386 (5.9+20140913-1) ...
+Setting up tabix (1.1-1) ...
+Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-2) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-11) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 3.2.0-4-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.24.51.20140903-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-14 gcc-4.9_4.9.1-14 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-14 libstdc++6_4.9.1-14 linux-libc-dev_3.16.2-3
+Package versions: apt_1.0.8 base-files_7.5 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140903-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-14 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_4 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -322,589 +328,1616 @@ Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.1
+dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying dynamic-build.patch
+dpkg-source: info: applying debian-changes
Check disc space
────────────────
+Sufficient free space for build
+
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=parallel=2
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=sid-i386-sbuild
+SCHROOT_CHROOT_NAME=sid-i386-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-i386-sbuild-813c0d07-75a0-43f9-aa37-749f9218ed0c
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
+dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.1
dpkg-buildpackage: host architecture i386
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j2 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f TAGS
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_auto_configure -a -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/i386-linux-gnu/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j2 HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_i386.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.19-1_i386.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0918
-
-samtools_0.1.19-1_i386.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: i386
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 8cb3c4917736e45c557b1b9b690bfd831d514914 564504 samtools_0.1.19-1_i386.deb
- 88c85415b2ca939d7553b847e3bb1a7e7e7203bd 127164 libbam-dev_0.1.19-1_i386.deb
-Checksums-Sha256:
- b816433ae0d856ccb4a0f4220ac5a32d1a3c254670ecc0807ef10f24f5dd3dd0 564504 samtools_0.1.19-1_i386.deb
- 5684aadde55d2d513b96aab8791e7c8018584618ddf65e87f498024007db0147 127164 libbam-dev_0.1.19-1_i386.deb
-Files:
- c3ae79838dad2598010a977afe2c9395 564504 science optional samtools_0.1.19-1_i386.deb
- a3a4e27aa92be780283eae154240d4d8 127164 libdevel optional libbam-dev_0.1.19-1_i386.deb
+padding.c:199:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
+ fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+ ^
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+misc/ace2sam.c: In function 'main':
+misc/ace2sam.c:112:13: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=]
+ fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
+ ^
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+test/merge/test_rtrans_build.c: In function 'main':
+test/merge/test_rtrans_build.c:79:29: warning: overflow in implicit constant conversion [-Woverflow]
+ const long GIMIC_SEED = 0x1234abcd330e;
+ ^
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+test/merge/test_trans_tbl_init.c: In function 'main':
+test/merge/test_trans_tbl_init.c:323:31: warning: overflow in implicit constant conversion [-Woverflow]
+ const long GIMMICK_SEED = 0x1234abcd330e;
+ ^
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/i386-linux-gnu/libhts.a -lhts -lcurses [...]
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/i386-linux-gnu/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+make[2]: Entering directory '/«PKGBUILDDIR»'
+REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/PHZ6a904Ap/bgzip.dat.gz
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/PHZ6a904Ap/bgzip.dat.gz
+.. ok
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/PHZ6a904Ap/bgzip.dat.gz
+.. ok
-samtools_0.1.19-1_i386.deb
-──────────────────────────
-
- new debian package, version 2.0.
- size 564504 bytes: control archive= 1932 bytes.
- 32 bytes, 1 lines conffiles
- 791 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1351
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: processing sequence alignments in SAM and BAM formats
- Samtools is a set of utilities that manipulate nucleotide sequence alignments
- in the binary BAM format. It imports from and exports to the ascii SAM
- (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- to retrieve reads in any regions swiftly. It is designed to work on a stream,
- and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/samtools/
--rwxr-xr-x root/root 9604 2013-03-30 09:18 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 9628 2013-03-30 09:18 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9628 2013-03-30 09:18 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 187448 2013-03-30 09:18 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 13728 2013-03-30 09:18 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 17896 2013-03-30 09:18 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 17840 2013-03-30 09:18 ./usr/lib/samtools/ace2sam
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/bin/
--rwxr-xr-x root/root 157732 2013-03-30 09:18 ./usr/bin/bcftools
--rwxr-xr-x root/root 26152 2013-03-30 09:18 ./usr/bin/razip
--rwxr-xr-x root/root 439700 2013-03-30 09:18 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 09:18 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2013-03-30 09:18 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/man/man1/
--rw-r--r-- root/root 10654 2013-03-30 09:18 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2013-03-30 09:18 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:18 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
-lrwxrwxrwx root/root 0 2013-03-30 09:18 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_i386.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 127164 bytes: control archive= 927 bytes.
- 711 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 405
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/
--rw-r--r-- root/root 291948 2013-03-30 09:18 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/include/samtools/
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
+/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
+/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /tmp/PHZ6a904Ap/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/PHZ6a904Ap/large_chrom.bam ref2
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/dat/large_chrom.out
+ /«PKGBUILDDIR»/test/dat/large_chrom.out.new
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/PHZ6a904Ap/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/PHZ6a904Ap/mpileup.bam.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/PHZ6a904Ap/mpileup.cram.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/PHZ6a904Ap/mpileup.bam.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/PHZ6a904Ap/mpileup.cram.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/PHZ6a904Ap/mpileup.cram.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/PHZ6a904Ap/mpileup.cram.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:1050-1060 /tmp/PHZ6a904Ap/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:1050-1060 /tmp/PHZ6a904Ap/mpileup.1.cram | grep -v mpileup
+test/test.pl: module IO::Pty not found; skipping usage tests
+.. ok
+
+test_usage:
+ samtools
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM
+ SAM files differ at /tmp/PHZ6a904Ap/view.test001.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test001.bam -b /tmp/PHZ6a904Ap/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test001.bam.sam /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 2: SAM -> uncompressed BAM .. ok
+
+ 3: uncompressed BAM -> SAM and compare
+ SAM files differ at /tmp/PHZ6a904Ap/view.test003.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test003.sam -h /tmp/PHZ6a904Ap/view.test002.bam
+
+
+.. failed ...
+
+ 4: SAM -> fast compressed BAM .. ok
+
+ 5: fast compressed BAM -> SAM and compare
+ SAM files differ at /tmp/PHZ6a904Ap/view.test005.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test005.sam -h /tmp/PHZ6a904Ap/view.test004.bam
+
+
+.. failed ...
+
+ 6: SAM -> CRAM -> SAM (UR header tags)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test006.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test006.cram -C /tmp/PHZ6a904Ap/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test006.cram.sam /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 7: SAM -> CRAM -> SAM (M5 header tags)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test007.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test007.cram -C /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test007.cram.sam /tmp/PHZ6a904Ap/view.test007.cram
+
+
+.. failed ...
+
+ 8: BAM -> CRAM with UR -> SAM
+ SAM files differ at /tmp/PHZ6a904Ap/view.test008.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test008.cram -C /tmp/PHZ6a904Ap/view.test001.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test008.cram.sam /tmp/PHZ6a904Ap/view.test008.cram
+
+
+.. failed ...
+
+ 9: SAM -> BAM (M5 header tags)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test009.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test009.bam -b /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test009.bam.sam /tmp/PHZ6a904Ap/view.test009.bam
+
+
+.. failed ...
+
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test010.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test010.cram -C /tmp/PHZ6a904Ap/view.test009.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test010.cram.sam /tmp/PHZ6a904Ap/view.test010.cram
+
+
+.. failed ...
+
+ 11: CRAM -> BAM with UR
+ SAM files differ at /tmp/PHZ6a904Ap/view.test011.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test011.bam -b /tmp/PHZ6a904Ap/view.test008.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test011.bam.sam /tmp/PHZ6a904Ap/view.test011.bam
+
+
+.. failed ...
+
+ 12: CRAM -> BAM with M5
+ SAM files differ at /tmp/PHZ6a904Ap/view.test012.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test012.bam -b /tmp/PHZ6a904Ap/view.test010.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test012.bam.sam /tmp/PHZ6a904Ap/view.test012.bam
+
+
+.. failed ...
+
+ 13: SAM -> SAM via stdout
+ SAM files differ at /tmp/PHZ6a904Ap/view.test013.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -h /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 14: SAM -> BAM via stdout .. ok
+
+ 15: SAM -> CRAM via stdout
+ SAM files differ at /tmp/PHZ6a904Ap/view.test015.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -C /tmp/PHZ6a904Ap/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test015.cram.sam /tmp/PHZ6a904Ap/view.test015.cram
+
+
+.. failed ...
+
+ 16: SAM from stdin -> SAM
+ SAM files differ at /tmp/PHZ6a904Ap/view.test016.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test016.sam -h -
+
+
+.. failed ...
+
+ 17: BAM from stdin -> SAM
+ SAM files differ at /tmp/PHZ6a904Ap/view.test017.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test017.sam -h -
+
+
+.. failed ...
+
+ 18: CRAM from stdin -> SAM
+ SAM files differ at /tmp/PHZ6a904Ap/view.test018.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test018.sam -h -
+
+
+.. failed ...
+
+ 19: samtools view -H (SAM input) .. ok
+
+ 20: samtools view -H (BAM input) .. ok
+
+ 21: samtools view -H (CRAM input) .. ok
+
+ 22: No headers (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test022.body : 6 / /tmp/PHZ6a904Ap/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test022.body /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 23: No headers (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test023.body : 6 / /tmp/PHZ6a904Ap/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test023.body /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 24: No headers (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test024.body : 6 / /tmp/PHZ6a904Ap/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test024.body /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 25: Filter -f 128 (SAM input) .. ok
+
+ 26: Count -f 128 (SAM input) .. ok
+
+ 27: Filter -f 128 (BAM input) .. ok
+
+ 28: Count -f 128 (BAM input) .. ok
+
+ 29: Filter -f 128 (CRAM input) .. ok
+
+ 30: Count -f 128 (CRAM input) .. ok
+
+ 31: Filter -F 128 (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test031.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test031.sam -h -F 128 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 32: Count -F 128 (SAM input) .. ok
+
+ 33: Filter -F 128 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test033.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test033.sam -h -F 128 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 34: Count -F 128 (BAM input) .. ok
+
+ 35: Filter -F 128 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test035.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test035.sam -h -F 128 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 36: Count -F 128 (CRAM input) .. ok
+
+ 37: Filter -F 128 -f 2 (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test037.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test037.sam -h -F 128 -f 2 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 38: Count -F 128 -f 2 (SAM input) .. ok
+
+ 39: Filter -F 128 -f 2 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test039.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test039.sam -h -F 128 -f 2 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 40: Count -F 128 -f 2 (BAM input) .. ok
+
+ 41: Filter -F 128 -f 2 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test041.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test041.sam -h -F 128 -f 2 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 42: Count -F 128 -f 2 (CRAM input) .. ok
+
+ 43: Filter -r grp2 (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test043.sam : 29 / /tmp/PHZ6a904Ap/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test043.sam -h -r grp2 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 44: Count -r grp2 (SAM input) .. ok
+
+ 45: Filter -r grp2 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test045.sam : 29 / /tmp/PHZ6a904Ap/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test045.sam -h -r grp2 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 46: Count -r grp2 (BAM input) .. ok
+
+ 47: Filter -r grp2 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test047.sam : 29 / /tmp/PHZ6a904Ap/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test047.sam -h -r grp2 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 48: Count -r grp2 (CRAM input) .. ok
+
+ 49: Filter -R /tmp/PHZ6a904Ap/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/PHZ6a904Ap/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/PHZ6a904Ap/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/PHZ6a904Ap/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/PHZ6a904Ap/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/PHZ6a904Ap/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test055.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test055.sam -h -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 56: Count -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test057.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test057.sam -h -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 58: Count -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test059.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test059.sam -h -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 60: Count -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test061.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test061.sam -h -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 62: Count -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test063.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test063.sam -h -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 64: Count -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test065.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test065.sam -h -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 66: Count -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (CRAM input).. ok
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 67: Filter -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test067.sam -h -l Library 2 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 68: Count -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 69: Filter -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test069.sam -h -l Library 2 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 70: Count -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 71: Filter -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test071.sam -h -l Library 2 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 72: Count -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. expected failure
+
+ 73: Filter -q 50 (SAM input) .. ok
+
+ 74: Count -q 50 (SAM input) .. ok
+
+ 75: Filter -q 50 (BAM input) .. ok
+
+ 76: Count -q 50 (BAM input) .. ok
+
+ 77: Filter -q 50 (CRAM input) .. ok
+
+ 78: Count -q 50 (CRAM input) .. ok
+
+ 79: Filter -q 99 (SAM input) .. ok
+
+ 80: Count -q 99 (SAM input) .. ok
+
+ 81: Filter -q 99 (BAM input) .. ok
+
+ 82: Count -q 99 (BAM input) .. ok
+
+ 83: Filter -q 99 (CRAM input) .. ok
+
+ 84: Count -q 99 (CRAM input) .. ok
+
+ 85: Filter -q 100 (SAM input) .. ok
+
+ 86: Count -q 100 (SAM input) .. ok
+
+ 87: Filter -q 100 (BAM input) .. ok
+
+ 88: Count -q 100 (BAM input) .. ok
+
+ 89: Filter -q 100 (CRAM input) .. ok
+
+ 90: Count -q 100 (CRAM input) .. ok
+
+ 91: Filter -x fa (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test091.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test091.sam -h -x fa /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 92: Count -x fa (SAM input) .. ok
+
+ 93: Filter -x fa (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test093.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test093.sam -h -x fa /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 94: Count -x fa (BAM input) .. ok
+
+ 95: Filter -x fa (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test095.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test095.sam -h -x fa /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 96: Count -x fa (CRAM input) .. ok
+
+ 97: Filter -x fa -x ha (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test097.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test097.sam -h -x fa -x ha /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 98: Count -x fa -x ha (SAM input) .. ok
+
+ 99: Filter -x fa -x ha (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test099.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test099.sam -h -x fa -x ha /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 100: Count -x fa -x ha (BAM input) .. ok
+
+ 101: Filter -x fa -x ha (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test101.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test101.sam -h -x fa -x ha /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 102: Count -x fa -x ha (CRAM input) .. ok
+
+ 103: Filter -x fa -r grp2 (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test103.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test103.sam -h -x fa -r grp2 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 104: Count -x fa -r grp2 (SAM input) .. ok
+
+ 105: Filter -x fa -r grp2 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test105.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test105.sam -h -x fa -r grp2 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 106: Count -x fa -r grp2 (BAM input) .. ok
+
+ 107: Filter -x fa -r grp2 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test107.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test107.sam -h -x fa -r grp2 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 108: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 109: Filter -x RG -r grp2 (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test109.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test109.sam -h -x RG -r grp2 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 110: Count -x RG -r grp2 (SAM input) .. ok
+
+ 111: Filter -x RG -r grp2 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test111.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test111.sam -h -x RG -r grp2 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 112: Count -x RG -r grp2 (BAM input) .. ok
+
+ 113: Filter -x RG -r grp2 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test113.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test113.sam -h -x RG -r grp2 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 114: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 115: Filter -m 10 (SAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test115.sam : 34 / /tmp/PHZ6a904Ap/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test115.sam -h -m 10 /tmp/PHZ6a904Ap/view.001.sam
+
+
+.. failed ...
+
+ 116: Count -m 10 (SAM input) .. ok
+
+ 117: Filter -m 10 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test117.sam : 34 / /tmp/PHZ6a904Ap/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test117.sam -h -m 10 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 118: Count -m 10 (BAM input) .. ok
+
+ 119: Filter -m 10 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test119.sam : 34 / /tmp/PHZ6a904Ap/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test119.sam -h -m 10 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 120: Count -m 10 (CRAM input) .. ok
+
+ 121: Filter -m 11 (SAM input) .. ok
+
+ 122: Count -m 11 (SAM input) .. ok
+
+ 123: Filter -m 11 (BAM input) .. ok
+
+ 124: Count -m 11 (BAM input) .. ok
+
+ 125: Filter -m 11 (CRAM input) .. ok
+
+ 126: Count -m 11 (CRAM input) .. ok
+
+ 127: Filter -m 15 (SAM input) .. ok
+
+ 128: Count -m 15 (SAM input) .. ok
+
+ 129: Filter -m 15 (BAM input) .. ok
+
+ 130: Count -m 15 (BAM input) .. ok
+
+ 131: Filter -m 15 (CRAM input) .. ok
+
+ 132: Count -m 15 (CRAM input) .. ok
+
+ 133: Filter -m 16 (SAM input) .. ok
+
+ 134: Count -m 16 (SAM input) .. ok
+
+ 135: Filter -m 16 (BAM input) .. ok
+
+ 136: Count -m 16 (BAM input) .. ok
+
+ 137: Filter -m 16 (CRAM input) .. ok
+
+ 138: Count -m 16 (CRAM input) .. ok
+
+ 139: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 140: Region Z (BAM input) .. ok
+
+ 141: Count Z (BAM input) .. ok
+
+ 142: Region Z (CRAM input) .. ok
+
+ 143: Count Z (CRAM input) .. ok
+
+ 144: Region Z:30 (BAM input) .. ok
+
+ 145: Count Z:30 (BAM input) .. ok
+
+ 146: Region Z:30 (CRAM input) .. ok
+
+ 147: Count Z:30 (CRAM input) .. ok
+
+ 148: Region Z:20-40 (BAM input) .. ok
+
+ 149: Count Z:20-40 (BAM input) .. ok
+
+ 150: Region Z:20-40 (CRAM input) .. ok
+
+ 151: Count Z:20-40 (CRAM input) .. ok
+
+ 152: Region ref1 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test152.sam : 34 / /tmp/PHZ6a904Ap/view.reg1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test152.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1
+
+
+.. failed ...
+
+ 153: Count ref1 (BAM input) .. ok
+
+ 154: Region ref1 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test154.sam : 34 / /tmp/PHZ6a904Ap/view.reg1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test154.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1
+
+
+.. failed ...
+
+ 155: Count ref1 (CRAM input) .. ok
+
+ 156: Region ref1:15 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test156.sam : 31 / /tmp/PHZ6a904Ap/view.reg2.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test156.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15
+
+
+.. failed ...
+
+ 157: Count ref1:15 (BAM input) .. ok
+
+ 158: Region ref1:15 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test158.sam : 31 / /tmp/PHZ6a904Ap/view.reg2.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test158.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15
+
+
+.. failed ...
+
+ 159: Count ref1:15 (CRAM input) .. ok
+
+ 160: Region ref1:15-45 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test160.sam : 31 / /tmp/PHZ6a904Ap/view.reg3.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test160.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45
+
+
+.. failed ...
+
+ 161: Count ref1:15-45 (BAM input) .. ok
+
+ 162: Region ref1:15-45 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test162.sam : 31 / /tmp/PHZ6a904Ap/view.reg3.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test162.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45
+
+
+.. failed ...
+
+ 163: Count ref1:15-45 (CRAM input) .. ok
+
+ 164: Region ref1:15-45 ref2 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test164.sam : 31 / /tmp/PHZ6a904Ap/view.reg4.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test164.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45 ref2
+
+
+.. failed ...
+
+ 165: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 166: Region ref1:15-45 ref2 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test166.sam : 31 / /tmp/PHZ6a904Ap/view.reg4.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test166.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45 ref2
+
+
+.. failed ...
+
+ 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 168: Region ref1:15-45 ref2:16 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test168.sam : 31 / /tmp/PHZ6a904Ap/view.reg5.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test168.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45 ref2:16
+
+
+.. failed ...
+
+ 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 170: Region ref1:15-45 ref2:16 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test170.sam : 31 / /tmp/PHZ6a904Ap/view.reg5.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test170.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45 ref2:16
+
+
+.. failed ...
+
+ 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 172: Region ref1:15-45 ref2:16-31 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test172.sam : 31 / /tmp/PHZ6a904Ap/view.reg6.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test172.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45 ref2:16-31
+
+
+.. failed ...
+
+ 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test174.sam : 31 / /tmp/PHZ6a904Ap/view.reg6.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test174.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45 ref2:16-31
+
+
+.. failed ...
+
+ 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 176: Region ref1:15-15 ref1:45-45 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test176.sam : 31 / /tmp/PHZ6a904Ap/view.reg7.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test176.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-15 ref1:45-45
+
+
+.. failed ...
+
+ 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test178.sam : 31 / /tmp/PHZ6a904Ap/view.reg7.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test178.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-15 ref1:45-45
+
+
+.. failed ...
+
+ 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 180: Region -f 128 ref1 (BAM input) .. ok
+
+ 181: Count -f 128 ref1 (BAM input) .. ok
+
+ 182: Region -f 128 ref1 (CRAM input) .. ok
+
+ 183: Count -f 128 ref1 (CRAM input) .. ok
+
+ 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 188: Region -r grp2 ref1:15-45 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test188.sam : 28 / /tmp/PHZ6a904Ap/view.reg10.sam : 28
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test188.sam -h -r grp2 /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45
+
+
+.. failed ...
+
+ 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 190: Region -r grp2 ref1:15-45 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test190.sam : 28 / /tmp/PHZ6a904Ap/view.reg10.sam : 28
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test190.sam -h -r grp2 /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45
+
+
+.. failed ...
+
+ 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test200.sam : 33 / /tmp/PHZ6a904Ap/view.bed1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test200.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test202.sam : 33 / /tmp/PHZ6a904Ap/view.bed1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test202.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test204.sam : 34 / /tmp/PHZ6a904Ap/view.bed2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test204.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test206.sam : 34 / /tmp/PHZ6a904Ap/view.bed2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test206.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test224.sam : 33 / /tmp/PHZ6a904Ap/view.bed1r1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test224.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/PHZ6a904Ap/view.test001.bam ref1:11-16
+
+
+.. failed ...
+
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test226.sam : 33 / /tmp/PHZ6a904Ap/view.bed1r1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test226.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/PHZ6a904Ap/view.test006.cram ref1:11-16
+
+
+.. failed ...
+
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test240.sam : 29 / /tmp/PHZ6a904Ap/view.bed1f3.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test240.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/PHZ6a904Ap/view.test001.bam
+
+
+.. failed ...
+
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test242.sam : 29 / /tmp/PHZ6a904Ap/view.bed1f3.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test242.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/PHZ6a904Ap/view.test006.cram
+
+
+.. failed ...
+
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 248: Make BAM with no M5/UR tags
+ SAM files differ at /tmp/PHZ6a904Ap/view.001.no_sq.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.001.no_sq.bam -b /tmp/PHZ6a904Ap/view.001.no_m5.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.001.no_sq.bam.sam /tmp/PHZ6a904Ap/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 249: Add @SQ with -t (SAM -> SAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test249.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test249.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.sam
+
+
+.. failed ...
+
+ 250: Add @SQ with -T (SAM -> SAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test250.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test250.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.sam
+
+
+.. failed ...
+
+ 251: Add @SQ with -t (BAM -> SAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test251.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test251.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 252: Add @SQ with -T (BAM -> SAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test252.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test252.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 253: Add @SQ with -t (SAM -> BAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test253.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test253.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test253.bam.sam /tmp/PHZ6a904Ap/view.test253.bam
+
+
+.. failed ...
+
+ 254: Add @SQ with -T (SAM -> BAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test254.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test254.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test254.bam.sam /tmp/PHZ6a904Ap/view.test254.bam
+
+
+.. failed ...
+
+ 255: Add @SQ with -t (BAM -> BAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test255.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test255.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test255.bam.sam /tmp/PHZ6a904Ap/view.test255.bam
+
+
+.. failed ...
+
+ 256: Add @SQ with -T (BAM -> BAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test256.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test256.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test256.bam.sam /tmp/PHZ6a904Ap/view.test256.bam
+
+
+.. failed ...
+
+ 257: Add @SQ with -t (SAM -> CRAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test257.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test257.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test257.cram.sam /tmp/PHZ6a904Ap/view.test257.cram
+
+
+.. failed ...
+
+ 258: Add @SQ with -T (SAM -> CRAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test258.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test258.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test258.cram.sam /tmp/PHZ6a904Ap/view.test258.cram
+
+
+.. failed ...
+
+ 259: Add @SQ with -t (BAM -> CRAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test259.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test259.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test259.cram.sam /tmp/PHZ6a904Ap/view.test259.cram
+
+
+.. failed ...
+
+ 260: Add @SQ with -T (BAM -> CRAM)
+ SAM files differ at /tmp/PHZ6a904Ap/view.test260.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test260.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test260.cram.sam /tmp/PHZ6a904Ap/view.test260.cram
+
+
+.. failed ...
+
+ 261: CIGAR B-operator removal .. ok
+
+ 262: Big SAM -> BAM .. ok
+
+ 263: Big SAM -> BAM (2 threads) .. ok
+
+ 264: Big SAM -> BAM (4 threads) .. ok
+
+ 265: Big SAM -> CRAM .. ok
+
+ 266: Big SAM -> CRAM (2 threads) .. ok
+
+ 267: Big SAM -> CRAM (4 threads) .. ok
+
+ 268: Subsample 0.2 (SAM input) ............ ok
+
+ 269: Subsample 0.5 (SAM input) ............ ok
+
+ 270: Subsample 0.8 (SAM input) ............ ok
+
+ 271: Subsample 0.2 (BAM input) ............ ok
+
+ 272: Subsample 0.5 (BAM input) ............ ok
+
+ 273: Subsample 0.8 (BAM input) ............ ok
+
+ 274: Subsample 0.2 (CRAM input) ............ ok
+
+ 275: Subsample 0.5 (CRAM input) ............ ok
+
+ 276: Subsample 0.8 (CRAM input) ............ ok
+
+test_cat:
+ Generating test data file .................. done
+ Generate BAM file #1 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #2 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #3 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #4 .. ok
+
+ 1: cat BAM files .. ok
+
+ 2: cat recompressed BAM files .. ok
+
+ 3: cat BAM files to stdout .. ok
+
+ 4: cat recompressed BAM files to stdout .. ok
+
+ 5: cat BAM files with new header .. ok
+
+ 6: cat recompressed BAM files with new header .. ok
+
+test_bam2fq:
+ Generate BAM file
+ SAM files differ at GLOB(0x940eafc) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/bam2fq.001.bam -b /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/PHZ6a904Ap/bam2fq.001.bam
+
+
+.. failed ...
+
+ Generate CRAM file
+ SAM files differ at GLOB(0x95099f4) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/bam2fq.001.cram -C /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/PHZ6a904Ap/bam2fq.001.cram
+
+
+.. failed ...
+
+[M::main_bam2fq] processed 36 reads
+ 1: bam2fq (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 2: bam2fq -n (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 3: bam2fq (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 4: bam2fq -n (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 5: bam2fq (CRAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 6: bam2fq -n (CRAM input) .. ok
+
+test_depad:
+ Generate BAM file .. ok
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/PHZ6a904Ap/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/PHZ6a904Ap/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/PHZ6a904Ap/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/PHZ6a904Ap/depad.001p.bam
+
+
+.. expected failure
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+/bin/bash: line 1: 21899 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/V6s2T3YPb4
+
+.. expected failure
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/tf0f5Fk0ku - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+
+.. expected failure
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/2_isize_overflow.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/3_reverse_read_pp_lt.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/4_reverse_read_pp_equal.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/5_ct.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
+.. ok
+
+test_idxstat:
+ /«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+
+Number of tests:
+ total .. 342
+ passed .. 237
+ failed .. 87
+ expected failure .. 18
+ unexpected pass .. 0
+
+make[2]: *** [test] Error 1
+Makefile:183: recipe for target 'test' failed
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+dh_auto_test: make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip returned exit code 2
+make[1]: *** [override_dh_auto_test] Error 2
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+debian/rules:18: recipe for target 'override_dh_auto_test' failed
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+debian/rules:6: recipe for target 'build-arch' failed
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20140925-0027
+
+Finished
+────────
+
+E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
+│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-9ec63e60-6331-45ff-ad27-68acd8c0fc8c/build/buildd-samtools_0.1.19-1-i386-yTX1S8
+Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Architecture: i386
-Build-Space: 13620
-Build-Time: 59
+Build Architecture: i386
+Build-Space: 20484
+Build-Time: 98
Distribution: sid
-Install-Time: 52
-Job: samtools_0.1.19-1
+Fail-Stage: build
+Host Architecture: i386
+Install-Time: 38
+Job: samtools_1.1-1
+Machine Architecture: amd64
Package: samtools
-Package-Time: 143
-Source-Version: 0.1.19-1
-Space: 13620
-Status: successful
-Version: 0.1.19-1
+Package-Time: 186
+Source-Version: 1.1-1
+Space: 20484
+Status: attempted
+Version: 1.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0918
-Build needed 00:02:23, 13620k disc space
-Signature with key 'DFABA12A' requested:
+Finished at 20140925-0027
+Build needed 00:03:06, 20484k disc space
diff --git a/info b/info
index 0b93a66..56fc7ff 100644
--- a/info
+++ b/info
@@ -1,13 +1,8 @@
-powerpc~1364634980~sid~successful
-s390~1364635066~sid~successful
-s390x~1364635068~sid~successful
-i386~1364635134~sid~successful
-ia64~1364635156~sid~successful
-kfreebsd-i386~1364635168~sid~successful
-sparc~1364635192~sid~failed
-kfreebsd-amd64~1364635194~sid~successful
-hurd-i386~1364635200~sid~successful
-armhf~1364635392~sid~successful
-mipsel~1364635510~sid~successful
-armel~1364636399~sid~failed
-mips~1364653370~sid~successful
+i386~1411604847~sid~failed
+kfreebsd-amd64~1411605089~sid~successful
+kfreebsd-i386~1411605287~sid~failed
+armel~1411609712~sid~failed
+mipsel~1411612103~sid~failed
+ppc64el~1411613735~sid~failed
+arm64~1411622963~sid~failed
+armel~1411693492~sid~failed
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index a9baa66..9c57b14 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,65 +1,74 @@
-From buildd at fano.debian.org Sat Mar 30 09:19:54 2013
+From buildd at fano.debian.org Thu Sep 25 00:31:28 2014
Return-path: <buildd at fano.debian.org>
-Received: from muffat.debian.org ([206.12.19.146])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1ULrx3-0002vl-LS
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:54 +0000
-Received: from fano.debian.org ([206.12.19.110])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
- by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
- (Exim 4.80) (envelope-from <buildd at fano.debian.org>)
- id 1ULrwz-0007Sg-Lo; Sat, 30 Mar 2013 09:19:49 +0000
-Received: from buildd by fano.debian.org with local (Exim 4.72)
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-Message-Id: <E1ULrwx-000LeB-NA at fano.debian.org>
-MIME-Version: 1.0
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Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 30 Mar 2013 09:19:47 +0000
+MIME-Version: 1.0
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+Date: Thu, 25 Sep 2014 00:31:25 +0000
From: buildd on fano <buildd at fano.debian.org>
-To: logs at buildd.debian.org,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on kfreebsd-amd64
- (dist=sid)
-Key-Id: 1B08409D
+To: christoph at debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_1.1-1 on kfreebsd-amd64
+ (dist=sid)
+Key-Id: 8C5D26F3
+Message-Id: <E1XWwxx-000Ir4-Vn at fano.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
+sbuild (Debian sbuild) 0.64.0 (17 May 2013) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (kfreebsd-amd64) 30 Mar 2013 09:16 ║
+║ samtools 1.1-1 (kfreebsd-amd64) 25 Sep 2014 00:27 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: kfreebsd-amd64
-Get:1 http://incoming.debian.org unstable Release.gpg [836 B]
-Get:2 http://mirror-ubc.debian.org unstable Release.gpg [836 B]
-Get:3 http://mirror-ubc.debian.org unstable Release [235 kB]
-Get:4 http://mirror-ubc.debian.org unstable/main Sources [6484 kB]
-Get:5 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
-Get:6 http://incoming.debian.org unstable Release [235 kB]
-Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [51.0 kB]
-Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
-Get:9 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5785 kB]
-Get:10 http://incoming.debian.org buildd-unstable Release [109 kB]
-Get:11 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:12 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [35.4 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:15 http://incoming.debian.org unstable/main kfreebsd-amd64 Packages [5785 kB]
-Get:16 http://incoming.debian.org unstable/contrib kfreebsd-amd64 Packages [35.4 kB]
-Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:20 http://incoming.debian.org buildd-unstable/main kfreebsd-amd64 Packages [13.4 kB]
-Get:21 http://incoming.debian.org buildd-unstable/contrib kfreebsd-amd64 Packages [14 B]
-Fetched 25.5 MB in 13s (1915 kB/s)
+Version: 1.1-1
+Source Version: 1.1-1
+Distribution: sid
+Machine Architecture: kfreebsd-amd64
+Host Architecture: kfreebsd-amd64
+Build Architecture: kfreebsd-amd64
+
+I: NOTICE: Log filtering will replace 'build/samtools-wRcBJH/samtools-1.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-wRcBJH' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ka-sbuild-1411604862-68022' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://mirror-ubc.debian.org unstable InRelease [233 kB]
+Get:2 http://mirror-ubc.debian.org unstable/main Sources [9757 kB]
+Get:3 http://ftp.debian.org unstable InRelease [233 kB]
+Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [67.0 kB]
+Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [127 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [8650 kB]
+Get:8 http://incoming.debian.org buildd-unstable/main Sources [450 kB]
+Get:9 http://ftp.debian.org unstable/main Sources [9757 kB]
+Get:10 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [46.3 kB]
+Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1082 B]
+Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [1643 B]
+Get:13 http://incoming.debian.org buildd-unstable/main kfreebsd-amd64 Packages [336 kB]
+Get:14 http://incoming.debian.org buildd-unstable/contrib kfreebsd-amd64 Packages [773 B]
+Get:15 http://ftp.debian.org unstable/contrib Sources [67.0 kB]
+Get:16 http://ftp.debian.org unstable/non-free Sources [127 kB]
+Get:17 http://ftp.debian.org unstable/main kfreebsd-amd64 Packages [8650 kB]
+Get:18 http://ftp.debian.org unstable/contrib kfreebsd-amd64 Packages [46.3 kB]
+Fetched 38.7 MB in 12s (3087 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,238 +86,239 @@ Download source files with APT
Reading package lists...
Building dependency tree...
+Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (444 kB/s)
+Need to get 4333 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
+Fetched 4333 kB in 5s (853 kB/s)
Download complete and in download only mode
Check arch
──────────
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-jaSah8/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
+│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
+Installing build dependencies
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Removing negative dependencies:
+Reading state information...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 38 not upgraded.
+Need to get 0 B/822 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ... 11188 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-1LN58k/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
Reading package lists...
-Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
+│ Install samtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.13-3.3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.10)
-e2fsprogs: already installed (1.42.5-1.1)
-findutils: already installed (4.4.2-5)
-freebsd-utils: already installed (9.0+ds1-11)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
+Installing build dependencies
Reading package lists...
Building dependency tree...
+Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5 libncurses5-dev libpipeline1 libtinfo-dev
+ libtinfo5 libunistring0 libxml2 man-db ncurses-bin po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
+ wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
+ www-browser libmail-box-perl
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
+ libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded.
-Need to get 10.4 MB of archives.
-After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.2.2-2 [39.9 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.22.2-1 [743 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-amd64 9.0.4 [210 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.6.3-3 [893 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.18.1.1-10 [27.2 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 1:5.11-2.1 [202 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-amd64 1:8.31-2 [247 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.8.0+dfsg1-7+nmu1 [914 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-amd64 3.0.10-3 [23.9 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.33.12+really2.32.4-5 [1831 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.6-2 [133 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5 [434 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-amd64 0.18.1.1-10 [145 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 1:5.11-2.1 [51.9 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.18.1.1-10 [153 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-amd64 1.3.2a-15 [104 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev kfreebsd-amd64 0.18.1.1-10 [27.0 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev kfreebsd-amd64 0.18.1.1-10 [184 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.18.1.1-10 [1805 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-amd64 1.55-3 [29.9 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 5.9-10 [105 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 5.9-10 [220 kB]
-Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.7.dfsg-13 [215 kB]
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
+ zlib1g-dev
+The following packages will be upgraded:
+ libncurses5 libtinfo5 ncurses-bin
+3 upgraded, 25 newly installed, 0 to remove and 35 not upgraded.
+Need to get 10.8 MB/10.8 MB of archives.
+After this operation, 30.2 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin kfreebsd-amd64 5.9+20140913-1 [347 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 kfreebsd-amd64 5.9+20140913-1 [283 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 kfreebsd-amd64 5.9+20140913-1 [96.8 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.3.1-1 [26.6 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.22.2-8 [1050 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-amd64 9.0.5 [211 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.7.0.1-1 [995 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.19.2-2 [30.8 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 1:5.19-2 [238 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.9.1+dfsg1-4 [801 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 kfreebsd-amd64 3.1-2 [19.3 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.42.0-1 [2480 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.8-3 [134 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 kfreebsd-amd64 1.1-1 [205 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5.2 [283 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 1:5.19-2 [58.2 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.19.2-2 [120 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.19.2-2 [1232 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev kfreebsd-amd64 1.1-1 [250 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 5.9+20140913-1 [76.7 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 5.9+20140913-1 [173 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main tabix kfreebsd-amd64 1.1-1 [190 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.8.dfsg-2 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.4 MB in 3s (3406 kB/s)
+Fetched 10.8 MB in 0s (15.4 MB/s)
+(Reading database ... 11188 files and directories currently installed.)
+Preparing to unpack .../ncurses-bin_5.9+20140913-1_kfreebsd-amd64.deb ...
+Unpacking ncurses-bin (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up ncurses-bin (5.9+20140913-1) ...
+(Reading database ... 11188 files and directories currently installed.)
+Preparing to unpack .../libtinfo5_5.9+20140913-1_kfreebsd-amd64.deb ...
+Unpacking libtinfo5:kfreebsd-amd64 (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up libtinfo5:kfreebsd-amd64 (5.9+20140913-1) ...
+Processing triggers for libc-bin (2.19-10) ...
+(Reading database ... 11188 files and directories currently installed.)
+Preparing to unpack .../libncurses5_5.9+20140913-1_kfreebsd-amd64.deb ...
+Unpacking libncurses5:kfreebsd-amd64 (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up libncurses5:kfreebsd-amd64 (5.9+20140913-1) ...
+Processing triggers for libc-bin (2.19-10) ...
Selecting previously unselected package libpipeline1:kfreebsd-amd64.
-(Reading database ... 11512 files and directories currently installed.)
-Unpacking libpipeline1:kfreebsd-amd64 (from .../libpipeline1_1.2.2-2_kfreebsd-amd64.deb) ...
+(Reading database ... 11188 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.3.1-1_kfreebsd-amd64.deb ...
+Unpacking libpipeline1:kfreebsd-amd64 (1.3.1-1) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_kfreebsd-amd64.deb) ...
+Preparing to unpack .../groff-base_1.22.2-8_kfreebsd-amd64.deb ...
+Unpacking groff-base (1.22.2-8) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_kfreebsd-amd64.deb) ...
+Preparing to unpack .../bsdmainutils_9.0.5_kfreebsd-amd64.deb ...
+Unpacking bsdmainutils (9.0.5) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_kfreebsd-amd64.deb) ...
+Preparing to unpack .../man-db_2.7.0.1-1_kfreebsd-amd64.deb ...
+Unpacking man-db (2.7.0.1-1) ...
Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
+Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
+Unpacking bash-completion (1:2.1-4) ...
Selecting previously unselected package libasprintf0c2:kfreebsd-amd64.
-Unpacking libasprintf0c2:kfreebsd-amd64 (from .../libasprintf0c2_0.18.1.1-10_kfreebsd-amd64.deb) ...
+Preparing to unpack .../libasprintf0c2_0.19.2-2_kfreebsd-amd64.deb ...
+Unpacking libasprintf0c2:kfreebsd-amd64 (0.19.2-2) ...
Selecting previously unselected package libmagic1:kfreebsd-amd64.
-Unpacking libmagic1:kfreebsd-amd64 (from .../libmagic1_1%3a5.11-2.1_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libpcre3:kfreebsd-amd64.
-Unpacking libpcre3:kfreebsd-amd64 (from .../libpcre3_1%3a8.31-2_kfreebsd-amd64.deb) ...
+Preparing to unpack .../libmagic1_1%3a5.19-2_kfreebsd-amd64.deb ...
+Unpacking libmagic1:kfreebsd-amd64 (1:5.19-2) ...
Selecting previously unselected package libxml2:kfreebsd-amd64.
-Unpacking libxml2:kfreebsd-amd64 (from .../libxml2_2.8.0+dfsg1-7+nmu1_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libffi5:kfreebsd-amd64.
-Unpacking libffi5:kfreebsd-amd64 (from .../libffi5_3.0.10-3_kfreebsd-amd64.deb) ...
+Preparing to unpack .../libxml2_2.9.1+dfsg1-4_kfreebsd-amd64.deb ...
+Unpacking libxml2:kfreebsd-amd64 (2.9.1+dfsg1-4) ...
+Selecting previously unselected package libffi6:kfreebsd-amd64.
+Preparing to unpack .../libffi6_3.1-2_kfreebsd-amd64.deb ...
+Unpacking libffi6:kfreebsd-amd64 (3.1-2) ...
Selecting previously unselected package libglib2.0-0:kfreebsd-amd64.
-Unpacking libglib2.0-0:kfreebsd-amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-5_kfreebsd-amd64.deb) ...
+Preparing to unpack .../libglib2.0-0_2.42.0-1_kfreebsd-amd64.deb ...
+Unpacking libglib2.0-0:kfreebsd-amd64 (2.42.0-1) ...
Selecting previously unselected package libcroco3:kfreebsd-amd64.
-Unpacking libcroco3:kfreebsd-amd64 (from .../libcroco3_0.6.6-2_kfreebsd-amd64.deb) ...
+Preparing to unpack .../libcroco3_0.6.8-3_kfreebsd-amd64.deb ...
+Unpacking libcroco3:kfreebsd-amd64 (0.6.8-3) ...
+Selecting previously unselected package libhts1:kfreebsd-amd64.
+Preparing to unpack .../libhts1_1.1-1_kfreebsd-amd64.deb ...
+Unpacking libhts1:kfreebsd-amd64 (1.1-1) ...
Selecting previously unselected package libunistring0:kfreebsd-amd64.
-Unpacking libunistring0:kfreebsd-amd64 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libgettextpo0:kfreebsd-amd64.
-Unpacking libgettextpo0:kfreebsd-amd64 (from .../libgettextpo0_0.18.1.1-10_kfreebsd-amd64.deb) ...
+Preparing to unpack .../libunistring0_0.9.3-5.2_kfreebsd-amd64.deb ...
+Unpacking libunistring0:kfreebsd-amd64 (0.9.3-5.2) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_kfreebsd-amd64.deb) ...
+Preparing to unpack .../file_1%3a5.19-2_kfreebsd-amd64.deb ...
+Unpacking file (1:5.19-2) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_kfreebsd-amd64.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libasprintf-dev:kfreebsd-amd64.
-Unpacking libasprintf-dev:kfreebsd-amd64 (from .../libasprintf-dev_0.18.1.1-10_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libgettextpo-dev:kfreebsd-amd64.
-Unpacking libgettextpo-dev:kfreebsd-amd64 (from .../libgettextpo-dev_0.18.1.1-10_kfreebsd-amd64.deb) ...
+Preparing to unpack .../gettext-base_0.19.2-2_kfreebsd-amd64.deb ...
+Unpacking gettext-base (0.19.2-2) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_kfreebsd-amd64.deb) ...
+Preparing to unpack .../gettext_0.19.2-2_kfreebsd-amd64.deb ...
+Unpacking gettext (0.19.2-2) ...
Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.1) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
+Unpacking po-debconf (1.0.16+nmu3) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_kfreebsd-amd64.deb) ...
+Preparing to unpack .../debhelper_9.20140817_all.deb ...
+Unpacking debhelper (9.20140817) ...
+Selecting previously unselected package libhts-dev:kfreebsd-amd64.
+Preparing to unpack .../libhts-dev_1.1-1_kfreebsd-amd64.deb ...
+Unpacking libhts-dev:kfreebsd-amd64 (1.1-1) ...
Selecting previously unselected package libtinfo-dev:kfreebsd-amd64.
-Unpacking libtinfo-dev:kfreebsd-amd64 (from .../libtinfo-dev_5.9-10_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_kfreebsd-amd64.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
+Preparing to unpack .../libtinfo-dev_5.9+20140913-1_kfreebsd-amd64.deb ...
+Unpacking libtinfo-dev:kfreebsd-amd64 (5.9+20140913-1) ...
+Selecting previously unselected package libncurses5-dev:kfreebsd-amd64.
+Preparing to unpack .../libncurses5-dev_5.9+20140913-1_kfreebsd-amd64.deb ...
+Unpacking libncurses5-dev:kfreebsd-amd64 (5.9+20140913-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.1-1_kfreebsd-amd64.deb ...
+Unpacking tabix (1.1-1) ...
Selecting previously unselected package zlib1g-dev:kfreebsd-amd64.
-Unpacking zlib1g-dev:kfreebsd-amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_kfreebsd-amd64.deb) ...
-Setting up libpipeline1:kfreebsd-amd64 (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_kfreebsd-amd64.deb ...
+Unpacking zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up libpipeline1:kfreebsd-amd64 (1.3.1-1) ...
+Setting up groff-base (1.22.2-8) ...
+Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:kfreebsd-amd64 (0.18.1.1-10) ...
-Setting up libmagic1:kfreebsd-amd64 (1:5.11-2.1) ...
-Setting up libpcre3:kfreebsd-amd64 (1:8.31-2) ...
-Setting up libxml2:kfreebsd-amd64 (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:kfreebsd-amd64 (3.0.10-3) ...
-Setting up libglib2.0-0:kfreebsd-amd64 (2.33.12+really2.32.4-5) ...
+Setting up man-db (2.7.0.1-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up bash-completion (1:2.1-4) ...
+Setting up libasprintf0c2:kfreebsd-amd64 (0.19.2-2) ...
+Setting up libmagic1:kfreebsd-amd64 (1:5.19-2) ...
+Setting up libxml2:kfreebsd-amd64 (2.9.1+dfsg1-4) ...
+Setting up libffi6:kfreebsd-amd64 (3.1-2) ...
+Setting up libglib2.0-0:kfreebsd-amd64 (2.42.0-1) ...
No schema files found: doing nothing.
-Setting up libcroco3:kfreebsd-amd64 (0.6.6-2) ...
-Setting up libunistring0:kfreebsd-amd64 (0.9.3-5) ...
-Setting up libgettextpo0:kfreebsd-amd64 (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:kfreebsd-amd64 (0.18.1.1-10) ...
-Setting up libgettextpo-dev:kfreebsd-amd64 (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
+Setting up libcroco3:kfreebsd-amd64 (0.6.8-3) ...
+Setting up libhts1:kfreebsd-amd64 (1.1-1) ...
+Setting up libunistring0:kfreebsd-amd64 (0.9.3-5.2) ...
+Setting up file (1:5.19-2) ...
+Setting up gettext-base (0.19.2-2) ...
+Setting up gettext (0.19.2-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:kfreebsd-amd64 (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Checking correctness of dependencies...
-Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 kfreebsd-kernel-headers_0.83 libc0.1-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.4 [...]
+Setting up po-debconf (1.0.16+nmu3) ...
+Setting up debhelper (9.20140817) ...
+Setting up libhts-dev:kfreebsd-amd64 (1.1-1) ...
+Setting up libtinfo-dev:kfreebsd-amd64 (5.9+20140913-1) ...
+Setting up libncurses5-dev:kfreebsd-amd64 (5.9+20140913-1) ...
+Setting up tabix (1.1-1) ...
+Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-10) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: GNU/kFreeBSD 9.0-2-amd64 kfreebsd-amd64 (x86_64)
+Toolchain package versions: binutils_2.24.51.20140903-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-12 gcc-4.9_4.9.1-12 kfreebsd-kernel-headers_10.0~5 libc0.1-dev_2.19-10 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12
+Package versions: apt_1.0.7 base-files_7.5 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140903-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-12 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_4 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -318,436 +328,1232 @@ Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.1
+dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying dynamic-build.patch
+dpkg-source: info: applying debian-changes
Check disc space
────────────────
+Sufficient free space for build
+
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=parallel=2
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=sid-kfreebsd-amd64-sbuild
+SCHROOT_CHROOT_NAME=sid-ka-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-ka-sbuild-1411604862-68022
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
+dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.1
dpkg-buildpackage: host architecture kfreebsd-amd64
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j2 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f TAGS
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_auto_configure -a -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j2 HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lcu [...]
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip
+make[2]: Entering directory '/«PKGBUILDDIR»'
+REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/2K2PBSgp_6/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/2K2PBSgp_6/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/2K2PBSgp_6/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /tmp/2K2PBSgp_6/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/2K2PBSgp_6/large_chrom.bam ref2
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/dat/large_chrom.out
+ /«PKGBUILDDIR»/test/dat/large_chrom.out.new
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/2K2PBSgp_6/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/2K2PBSgp_6/mpileup.bam.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/2K2PBSgp_6/mpileup.bam.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/2K2PBSgp_6/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/2K2PBSgp_6/mpileup.1.cram | grep -v mpileup
+test/test.pl: module IO::Pty not found; skipping usage tests
+.. ok
+
+test_usage:
+ samtools
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
+
+ 2: SAM -> uncompressed BAM .. ok
+
+ 3: uncompressed BAM -> SAM and compare .. ok
+
+ 4: SAM -> fast compressed BAM .. ok
+
+ 5: fast compressed BAM -> SAM and compare .. ok
+
+ 6: SAM -> CRAM -> SAM (UR header tags) .. ok
+
+ 7: SAM -> CRAM -> SAM (M5 header tags) .. ok
+
+ 8: BAM -> CRAM with UR -> SAM .. ok
+
+ 9: SAM -> BAM (M5 header tags) .. ok
+
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
+
+ 11: CRAM -> BAM with UR .. ok
+
+ 12: CRAM -> BAM with M5 .. ok
+
+ 13: SAM -> SAM via stdout .. ok
+
+ 14: SAM -> BAM via stdout .. ok
+
+ 15: SAM -> CRAM via stdout .. ok
+
+ 16: SAM from stdin -> SAM .. ok
+
+ 17: BAM from stdin -> SAM .. ok
+
+ 18: CRAM from stdin -> SAM .. ok
+
+ 19: samtools view -H (SAM input) .. ok
+
+ 20: samtools view -H (BAM input) .. ok
+
+ 21: samtools view -H (CRAM input) .. ok
+
+ 22: No headers (SAM input) .. ok
+
+ 23: No headers (BAM input) .. ok
+
+ 24: No headers (CRAM input) .. ok
+
+ 25: Filter -f 128 (SAM input) .. ok
+
+ 26: Count -f 128 (SAM input) .. ok
+
+ 27: Filter -f 128 (BAM input) .. ok
+
+ 28: Count -f 128 (BAM input) .. ok
+
+ 29: Filter -f 128 (CRAM input) .. ok
+
+ 30: Count -f 128 (CRAM input) .. ok
+
+ 31: Filter -F 128 (SAM input) .. ok
+
+ 32: Count -F 128 (SAM input) .. ok
+
+ 33: Filter -F 128 (BAM input) .. ok
+
+ 34: Count -F 128 (BAM input) .. ok
+
+ 35: Filter -F 128 (CRAM input) .. ok
+
+ 36: Count -F 128 (CRAM input) .. ok
+
+ 37: Filter -F 128 -f 2 (SAM input) .. ok
+
+ 38: Count -F 128 -f 2 (SAM input) .. ok
+
+ 39: Filter -F 128 -f 2 (BAM input) .. ok
+
+ 40: Count -F 128 -f 2 (BAM input) .. ok
+
+ 41: Filter -F 128 -f 2 (CRAM input) .. ok
+
+ 42: Count -F 128 -f 2 (CRAM input) .. ok
+
+ 43: Filter -r grp2 (SAM input) .. ok
+
+ 44: Count -r grp2 (SAM input) .. ok
+
+ 45: Filter -r grp2 (BAM input) .. ok
+
+ 46: Count -r grp2 (BAM input) .. ok
+
+ 47: Filter -r grp2 (CRAM input) .. ok
+
+ 48: Count -r grp2 (CRAM input) .. ok
+
+ 49: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (SAM input).. ok
+
+ 56: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (BAM input).. ok
+
+ 58: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 60: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input).. ok
+
+ 62: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input).. ok
+
+ 64: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input).. ok
+
+ 66: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input).. ok
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 67: Filter -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test067.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 68: Count -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 69: Filter -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test069.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 70: Count -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 71: Filter -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test071.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.test006.cram
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 72: Count -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.test006.cram
+
+
+.. expected failure
+
+ 73: Filter -q 50 (SAM input) .. ok
+
+ 74: Count -q 50 (SAM input) .. ok
+
+ 75: Filter -q 50 (BAM input) .. ok
+
+ 76: Count -q 50 (BAM input) .. ok
+
+ 77: Filter -q 50 (CRAM input) .. ok
+
+ 78: Count -q 50 (CRAM input) .. ok
+
+ 79: Filter -q 99 (SAM input) .. ok
+
+ 80: Count -q 99 (SAM input) .. ok
+
+ 81: Filter -q 99 (BAM input) .. ok
+
+ 82: Count -q 99 (BAM input) .. ok
+
+ 83: Filter -q 99 (CRAM input) .. ok
+
+ 84: Count -q 99 (CRAM input) .. ok
+
+ 85: Filter -q 100 (SAM input) .. ok
+
+ 86: Count -q 100 (SAM input) .. ok
+
+ 87: Filter -q 100 (BAM input) .. ok
+
+ 88: Count -q 100 (BAM input) .. ok
+
+ 89: Filter -q 100 (CRAM input) .. ok
+
+ 90: Count -q 100 (CRAM input) .. ok
+
+ 91: Filter -x fa (SAM input) .. ok
+
+ 92: Count -x fa (SAM input) .. ok
+
+ 93: Filter -x fa (BAM input) .. ok
+
+ 94: Count -x fa (BAM input) .. ok
+
+ 95: Filter -x fa (CRAM input) .. ok
+
+ 96: Count -x fa (CRAM input) .. ok
+
+ 97: Filter -x fa -x ha (SAM input) .. ok
+
+ 98: Count -x fa -x ha (SAM input) .. ok
+
+ 99: Filter -x fa -x ha (BAM input) .. ok
+
+ 100: Count -x fa -x ha (BAM input) .. ok
+
+ 101: Filter -x fa -x ha (CRAM input) .. ok
+
+ 102: Count -x fa -x ha (CRAM input) .. ok
+
+ 103: Filter -x fa -r grp2 (SAM input) .. ok
+
+ 104: Count -x fa -r grp2 (SAM input) .. ok
+
+ 105: Filter -x fa -r grp2 (BAM input) .. ok
+
+ 106: Count -x fa -r grp2 (BAM input) .. ok
+
+ 107: Filter -x fa -r grp2 (CRAM input) .. ok
+
+ 108: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 109: Filter -x RG -r grp2 (SAM input) .. ok
+
+ 110: Count -x RG -r grp2 (SAM input) .. ok
+
+ 111: Filter -x RG -r grp2 (BAM input) .. ok
+
+ 112: Count -x RG -r grp2 (BAM input) .. ok
+
+ 113: Filter -x RG -r grp2 (CRAM input) .. ok
+
+ 114: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 115: Filter -m 10 (SAM input) .. ok
+
+ 116: Count -m 10 (SAM input) .. ok
+
+ 117: Filter -m 10 (BAM input) .. ok
+
+ 118: Count -m 10 (BAM input) .. ok
+
+ 119: Filter -m 10 (CRAM input) .. ok
+
+ 120: Count -m 10 (CRAM input) .. ok
+
+ 121: Filter -m 11 (SAM input) .. ok
+
+ 122: Count -m 11 (SAM input) .. ok
+
+ 123: Filter -m 11 (BAM input) .. ok
+
+ 124: Count -m 11 (BAM input) .. ok
+
+ 125: Filter -m 11 (CRAM input) .. ok
+
+ 126: Count -m 11 (CRAM input) .. ok
+
+ 127: Filter -m 15 (SAM input) .. ok
+
+ 128: Count -m 15 (SAM input) .. ok
+
+ 129: Filter -m 15 (BAM input) .. ok
+
+ 130: Count -m 15 (BAM input) .. ok
+
+ 131: Filter -m 15 (CRAM input) .. ok
+
+ 132: Count -m 15 (CRAM input) .. ok
+
+ 133: Filter -m 16 (SAM input) .. ok
+
+ 134: Count -m 16 (SAM input) .. ok
+
+ 135: Filter -m 16 (BAM input) .. ok
+
+ 136: Count -m 16 (BAM input) .. ok
+
+ 137: Filter -m 16 (CRAM input) .. ok
+
+ 138: Count -m 16 (CRAM input) .. ok
+
+ 139: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 140: Region Z (BAM input) .. ok
+
+ 141: Count Z (BAM input) .. ok
+
+ 142: Region Z (CRAM input) .. ok
+
+ 143: Count Z (CRAM input) .. ok
+
+ 144: Region Z:30 (BAM input) .. ok
+
+ 145: Count Z:30 (BAM input) .. ok
+
+ 146: Region Z:30 (CRAM input) .. ok
+
+ 147: Count Z:30 (CRAM input) .. ok
+
+ 148: Region Z:20-40 (BAM input) .. ok
+
+ 149: Count Z:20-40 (BAM input) .. ok
+
+ 150: Region Z:20-40 (CRAM input) .. ok
+
+ 151: Count Z:20-40 (CRAM input) .. ok
+
+ 152: Region ref1 (BAM input) .. ok
+
+ 153: Count ref1 (BAM input) .. ok
+
+ 154: Region ref1 (CRAM input) .. ok
+
+ 155: Count ref1 (CRAM input) .. ok
+
+ 156: Region ref1:15 (BAM input) .. ok
+
+ 157: Count ref1:15 (BAM input) .. ok
+
+ 158: Region ref1:15 (CRAM input) .. ok
+
+ 159: Count ref1:15 (CRAM input) .. ok
+
+ 160: Region ref1:15-45 (BAM input) .. ok
+
+ 161: Count ref1:15-45 (BAM input) .. ok
+
+ 162: Region ref1:15-45 (CRAM input) .. ok
+
+ 163: Count ref1:15-45 (CRAM input) .. ok
+
+ 164: Region ref1:15-45 ref2 (BAM input) .. ok
+
+ 165: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+
+ 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 180: Region -f 128 ref1 (BAM input) .. ok
+
+ 181: Count -f 128 ref1 (BAM input) .. ok
+
+ 182: Region -f 128 ref1 (CRAM input) .. ok
+
+ 183: Count -f 128 ref1 (CRAM input) .. ok
+
+ 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 248: Make BAM with no M5/UR tags .. ok
+
+ 249: Add @SQ with -t (SAM -> SAM) .. ok
+
+ 250: Add @SQ with -T (SAM -> SAM) .. ok
+
+ 251: Add @SQ with -t (BAM -> SAM) .. ok
+
+ 252: Add @SQ with -T (BAM -> SAM) .. ok
+
+ 253: Add @SQ with -t (SAM -> BAM) .. ok
+
+ 254: Add @SQ with -T (SAM -> BAM) .. ok
+
+ 255: Add @SQ with -t (BAM -> BAM) .. ok
+
+ 256: Add @SQ with -T (BAM -> BAM) .. ok
+
+ 257: Add @SQ with -t (SAM -> CRAM) .. ok
+
+ 258: Add @SQ with -T (SAM -> CRAM) .. ok
+
+ 259: Add @SQ with -t (BAM -> CRAM) .. ok
+
+ 260: Add @SQ with -T (BAM -> CRAM) .. ok
+
+ 261: CIGAR B-operator removal .. ok
+
+ 262: Big SAM -> BAM .. ok
+
+ 263: Big SAM -> BAM (2 threads) .. ok
+
+ 264: Big SAM -> BAM (4 threads) .. ok
+
+ 265: Big SAM -> CRAM .. ok
+
+ 266: Big SAM -> CRAM (2 threads) .. ok
+
+ 267: Big SAM -> CRAM (4 threads) .. ok
+
+ 268: Subsample 0.2 (SAM input) ............ ok
+
+ 269: Subsample 0.5 (SAM input) ............ ok
+
+ 270: Subsample 0.8 (SAM input) ............ ok
+
+ 271: Subsample 0.2 (BAM input) ............ ok
+
+ 272: Subsample 0.5 (BAM input) ............ ok
+
+ 273: Subsample 0.8 (BAM input) ............ ok
+
+ 274: Subsample 0.2 (CRAM input) ............ ok
+
+ 275: Subsample 0.5 (CRAM input) ............ ok
+
+ 276: Subsample 0.8 (CRAM input) ............ ok
+
+test_cat:
+ Generating test data file .................. done
+ Generate BAM file #1 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #2 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #3 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #4 .. ok
+
+ 1: cat BAM files .. ok
+
+ 2: cat recompressed BAM files .. ok
+
+ 3: cat BAM files to stdout .. ok
+
+ 4: cat recompressed BAM files to stdout .. ok
+
+ 5: cat BAM files with new header .. ok
+
+ 6: cat recompressed BAM files with new header .. ok
+
+test_bam2fq:
+ Generate BAM file .. ok
+
+ Generate CRAM file .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 1: bam2fq (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 2: bam2fq -n (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 3: bam2fq (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 4: bam2fq -n (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 5: bam2fq (CRAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 6: bam2fq -n (CRAM input) .. ok
+
+test_depad:
+ Generate BAM file .. ok
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/2K2PBSgp_6/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/2K2PBSgp_6/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/2K2PBSgp_6/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/2K2PBSgp_6/depad.001p.bam
+
+
+.. expected failure
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+/bin/bash: line 1: 70698 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/j8G9qPU9yq
+
+.. expected failure
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/qbbLiy2S7U - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+
+.. expected failure
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/2_isize_overflow.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/3_reverse_read_pp_lt.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/4_reverse_read_pp_equal.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/5_ct.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
+.. ok
+
+test_idxstat:
+ /«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+
+Number of tests:
+ total .. 342
+ passed .. 324
+ failed .. 0
+ expected failure .. 18
+ unexpected pass .. 0
+
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_pretty_header
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh
+Samtools mpileup tests:
+
+EXPECTED FAIL: Task failed, but expected to fail;
+when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
+
+Expected passes: 123
+Unexpected passes: 0
+Expected failures: 1
+Unexpected failures: 0
+=> PASS
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
+dh binary-arch --parallel
+ dh_testroot -a -O--parallel
+ dh_prep -a -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a
+ install -d debian/samtools
+ make -j2 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_install -a -O--parallel
+ install -d debian/samtools//usr
+ cp -a debian/tmp/usr/bin debian/samtools//usr/
+ install -d debian/samtools//usr/share/man
+ cp -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ dh_installdocs -a -O--parallel
+ install -g 0 -o 0 -d debian/samtools/usr/share/doc/samtools
+ cp -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ dh_installchangelogs -a -O--parallel
+ install -o 0 -g 0 -p -m644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ cd '/«PKGBUILDDIR»'
+ dh_fixperms -a -O--parallel
+ find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/samtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/samtools/usr/share/doc -type f ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/lib/x86_64-kfreebsd-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/samtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
+ dh_strip -a -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -o 0 -g 0 -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_kfreebsd-amd64.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.19-1_kfreebsd-amd64.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
+ chmod 644 debian/samtools/DEBIAN/control
+ chown 0:0 debian/samtools/DEBIAN/control
+ dh_md5sums -a -O--parallel
+ (cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/samtools/DEBIAN/md5sums
+ chown 0:0 debian/samtools/DEBIAN/md5sums
+ dh_builddeb -a -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package `samtools' in `../samtools_1.1-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_1.1-1_kfreebsd-amd64.changes
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.1
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0919
+Build finished at 20140925-0031
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.1-1_kfreebsd-amd64.changes:
+──────────────────────────────────────
-samtools_0.1.19-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
+Date: Thu, 25 Sep 2014 09:04:20 +0900
Source: samtools
-Binary: samtools libbam-dev
+Binary: samtools samtools-test
Architecture: kfreebsd-amd64
-Version: 0.1.19-1
+Version: 1.1-1
Distribution: sid
-Urgency: low
+Urgency: medium
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
+Description:
samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
+ samtools-test - test files for the samtools package.
+Changes:
+ samtools (1.1-1) unstable; urgency=medium
.
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- e6b77d210ee76ccaceb71d1a49773e310f3689dc 561946 samtools_0.1.19-1_kfreebsd-amd64.deb
- bc07e63bff213ff9cbcbfba001b5cda8ecdbc80f 123294 libbam-dev_0.1.19-1_kfreebsd-amd64.deb
-Checksums-Sha256:
- 5db3eb47c85a70f9b85565411e8f9479a777bc02cfe3150015303c35e6b3488a 561946 samtools_0.1.19-1_kfreebsd-amd64.deb
- ea157bd5664ee38511f9c3839df6a152d7a55346648c2d781c7cf4eabac7f660 123294 libbam-dev_0.1.19-1_kfreebsd-amd64.deb
-Files:
- 9c22dfdef81ef7a079844de427d336c5 561946 science optional samtools_0.1.19-1_kfreebsd-amd64.deb
- e387a1b9b0891720e37e44a27f2854cc 123294 libdevel optional libbam-dev_0.1.19-1_kfreebsd-amd64.deb
+ c448d48 Merge tag '1.1' into debian/unstable
+ d12ab1e Merge branch 'develop' into debian/unstable to solve issue
+ with regression tests needing a pseudo-terminal.
+ See https://github.com/samtools/samtools/issues/300
+ c87f8ce Add autopkg tests.
+ 7c50b7b Removed python-wrong-path-for-interpreter.patch
+ (issue solved upstream).
+Checksums-Sha1:
+ b6e1ad13e7adbb686479035064d939bc6b756735 376830 samtools_1.1-1_kfreebsd-amd64.deb
+Checksums-Sha256:
+ 6ce726976ac08ee869cc1814cbc87d52d9efc7b6c2328daadc14e0cbf349cecb 376830 samtools_1.1-1_kfreebsd-amd64.deb
+Files:
+ d0969c084ef2f415726914fc1baffe1d 376830 science optional samtools_1.1-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.19-1_kfreebsd-amd64.deb
-────────────────────────────────────
+samtools_1.1-1_kfreebsd-amd64.deb
+─────────────────────────────────
new debian package, version 2.0.
- size 561946 bytes: control archive= 1937 bytes.
- 32 bytes, 1 lines conffiles
- 803 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
+ size 376830 bytes: control archive=1566 bytes.
+ 815 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
Package: samtools
- Version: 0.1.19-1
+ Version: 1.1-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1267
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
+ Installed-Size: 1008
+ Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
+ Recommends: python
Section: science
Priority: optional
- Homepage: http://samtools.sourceforge.net
+ Homepage: http://www.htslib.org/
Description: processing sequence alignments in SAM and BAM formats
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
@@ -755,143 +1561,77 @@ samtools_0.1.19-1_kfreebsd-amd64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 09:19 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2013-03-30 09:19 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 09:19 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 09:19 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:19 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/bin/
--rwxr-xr-x root/root 154664 2013-03-30 09:19 ./usr/bin/bcftools
--rwxr-xr-x root/root 27032 2013-03-30 09:19 ./usr/bin/razip
--rwxr-xr-x root/root 416672 2013-03-30 09:19 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/samtools/
--rwxr-xr-x root/root 18680 2013-03-30 09:19 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 22696 2013-03-30 09:19 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 172720 2013-03-30 09:19 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 10368 2013-03-30 09:19 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10368 2013-03-30 09:19 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 14472 2013-03-30 09:19 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 10320 2013-03-30 09:19 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_kfreebsd-amd64.deb
-──────────────────────────────────────
-
- new debian package, version 2.0.
- size 123294 bytes: control archive= 934 bytes.
- 721 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: kfreebsd-amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 407
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/
--rw-r--r-- root/root 326938 2013-03-30 09:19 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/include/samtools/
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2014-09-25 00:31 ./
+drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/
+drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/bin/
+-rwxr-xr-x root/root 767928 2014-09-25 00:31 ./usr/bin/samtools
+-rwxr-xr-x root/root 22664 2014-09-25 00:31 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 10336 2014-09-25 00:31 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10336 2014-09-25 00:31 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14440 2014-09-25 00:31 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10280 2014-09-25 00:31 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 22752 2014-09-25 00:31 ./usr/bin/wgsim
+-rwxr-xr-x root/root 5328 2014-09-19 15:51 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2014-09-19 15:51 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2014-09-19 15:51 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2014-09-19 15:51 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 6773 2014-09-19 15:51 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48023 2014-09-19 15:51 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2014-09-19 15:51 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2014-09-19 15:51 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 16478 2014-09-19 15:51 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 10789 2014-09-19 15:51 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2014-09-19 15:51 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2014-09-19 15:51 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 4157 2014-09-19 15:51 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2014-09-19 15:51 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/
+drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/man/man1/
+-rw-r--r-- root/root 12774 2014-09-25 00:31 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2014-09-19 15:51 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2014-09-24 23:56 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2014-09-24 23:56 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3462 2014-09-24 23:56 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 3270 2014-09-25 00:05 ./usr/share/doc/samtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
+│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
+│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1364634988-80311/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o
+Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Architecture: kfreebsd-amd64
-Build-Space: 16316
-Build-Time: 67
+Build Architecture: kfreebsd-amd64
+Build-Space: 15254
+Build-Time: 132
Distribution: sid
-Install-Time: 33
-Job: samtools_0.1.19-1
+Host Architecture: kfreebsd-amd64
+Install-Time: 32
+Job: samtools_1.1-1
+Machine Architecture: kfreebsd-amd64
Package: samtools
-Package-Time: 197
-Source-Version: 0.1.19-1
-Space: 16316
+Package-Time: 217
+Source-Version: 1.1-1
+Space: 15254
Status: successful
-Version: 0.1.19-1
+Version: 1.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0919
-Build needed 00:03:17, 16316k disc space
-Signature with key '1B08409D' requested:
+Finished at 20140925-0031
+Build needed 00:03:37, 15254k disc space
+Signature with key '8C5D26F3' requested:
+ signfile /home/buildd/build/samtools_1.1-1_kfreebsd-amd64.changes 8C5D26F3
+
+Successfully signed changes file
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index c66f0dc..d9a73f8 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,66 +1,73 @@
-From buildd at finzi.debian.org Sat Mar 30 09:19:27 2013
+From buildd at finzi.debian.org Thu Sep 25 00:34:46 2014
Return-path: <buildd at finzi.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1ULrwd-0002uH-7n
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:27 +0000
-Received: from finzi.debian.org ([206.12.19.111])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1ULrwb-0001bT-UT; Sat, 30 Mar 2013 09:19:26 +0000
-Received: from buildd by finzi.debian.org with local (Exim 4.72)
- (envelope-from <buildd at finzi.debian.org>)
- id 1ULrwZ-0008MU-BL; Sat, 30 Mar 2013 09:19:23 +0000
-Message-Id: <E1ULrwZ-0008MU-BL at finzi.debian.org>
-MIME-Version: 1.0
+Received: from muffat.debian.org ([2607:f8f0:610:4000:6564:a62:ce0c:1392])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
+ by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at finzi.debian.org>)
+ id 1XWx1C-0008E6-Df
+ for logs at buildd.debian.org; Thu, 25 Sep 2014 00:34:46 +0000
+Received: from finzi.debian.org ([2607:f8f0:610:4000:6564:a62:19:111])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
+ by muffat.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at finzi.debian.org>)
+ id 1XWx1A-0005sy-MD; Thu, 25 Sep 2014 00:34:44 +0000
+Received: from buildd by finzi.debian.org with local (Exim 4.80)
+ (envelope-from <buildd at finzi.debian.org>)
+ id 1XWx19-000Ash-NH; Thu, 25 Sep 2014 00:34:43 +0000
Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 30 Mar 2013 09:19:23 +0000
+MIME-Version: 1.0
+X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
+Date: Thu, 25 Sep 2014 00:34:43 +0000
From: buildd on finzi <buildd at finzi.debian.org>
-To: logs at buildd.debian.org,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on kfreebsd-i386
- (dist=sid)
-Key-Id: B31C365A
+To: christoph at debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_1.1-1 on kfreebsd-i386 (dist=sid)
+Key-Id: A10F7C65
+Message-Id: <E1XWx19-000Ash-NH at finzi.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
+sbuild (Debian sbuild) 0.64.0 (17 May 2013) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (kfreebsd-i386) 30 Mar 2013 09:15 ║
+║ samtools 1.1-1 (kfreebsd-i386) 25 Sep 2014 00:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: kfreebsd-i386
-Get:1 http://incoming.debian.org unstable Release.gpg [836 B]
-Get:2 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
-Get:3 http://incoming.debian.org unstable Release [235 kB]
-Get:4 http://mirror-ubc.debian.org unstable Release.gpg [836 B]
-Get:5 http://incoming.debian.org buildd-unstable Release [109 kB]
-Get:6 http://mirror-ubc.debian.org unstable Release [235 kB]
-Get:7 http://mirror-ubc.debian.org unstable/main Sources [6484 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib Sources [51.0 kB]
-Get:10 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [5786 kB]
-Get:12 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [35.4 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:15 http://incoming.debian.org unstable/main kfreebsd-i386 Packages [5786 kB]
-Get:16 http://incoming.debian.org unstable/contrib kfreebsd-i386 Packages [35.4 kB]
-Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:20 http://incoming.debian.org buildd-unstable/main kfreebsd-i386 Packages [13.7 kB]
-Get:21 http://incoming.debian.org buildd-unstable/contrib kfreebsd-i386 Packages [14 B]
-Fetched 25.5 MB in 16s (1552 kB/s)
+Version: 1.1-1
+Source Version: 1.1-1
+Distribution: sid
+Machine Architecture: kfreebsd-i386
+Host Architecture: kfreebsd-i386
+Build Architecture: kfreebsd-i386
+
+I: NOTICE: Log filtering will replace 'build/samtools-qc6QH2/samtools-1.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-qc6QH2' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ki-sbuild-1411604684-24335' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://mirror-ubc.debian.org unstable InRelease [233 kB]
+Get:2 http://mirror-ubc.debian.org unstable/main Sources [7548 kB]
+Get:3 http://ftp.debian.org unstable InRelease [233 kB]
+Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [57.1 kB]
+Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [107 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [6486 kB]
+Get:8 http://ftp.debian.org unstable/main Sources [7548 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [39.7 kB]
+Get:10 http://incoming.debian.org buildd-unstable/main Sources [358 kB]
+Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1136 B]
+Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
+Get:13 http://incoming.debian.org buildd-unstable/main kfreebsd-i386 Packages [291 kB]
+Get:14 http://incoming.debian.org buildd-unstable/contrib kfreebsd-i386 Packages [844 B]
+Get:15 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
+Get:16 http://ftp.debian.org unstable/non-free Sources [107 kB]
+Get:17 http://ftp.debian.org unstable/main kfreebsd-i386 Packages [6486 kB]
+Get:18 http://ftp.debian.org unstable/contrib kfreebsd-i386 Packages [39.7 kB]
+Fetched 29.7 MB in 1min 7s (440 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,238 +85,239 @@ Download source files with APT
Reading package lists...
Building dependency tree...
+Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (432 kB/s)
+Need to get 4333 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
+Fetched 4333 kB in 15s (272 kB/s)
Download complete and in download only mode
Check arch
──────────
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-VZrg5j/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
+│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
+Installing build dependencies
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
-Removing negative dependencies:
+Reading state information...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 66 not upgraded.
+Need to get 0 B/822 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ... 10755 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-ZiCUyo/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
Reading package lists...
-Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
-Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
+│ Install samtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.13-3.3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.10)
-e2fsprogs: already installed (1.42.5-1.1)
-findutils: already installed (4.4.2-5)
-freebsd-utils: already installed (9.0+ds1-10)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
+Installing build dependencies
Reading package lists...
Building dependency tree...
+Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5 libncurses5-dev libpipeline1 libtinfo-dev
+ libtinfo5 libunistring0 libxml2 man-db ncurses-bin po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
+ wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
+ www-browser libmail-box-perl
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
+ libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 3 not upgraded.
-Need to get 10.2 MB of archives.
-After this operation, 27.3 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.2-2 [38.9 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.22.2-1 [733 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.4 [205 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.6.3-3 [889 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.18.1.1-10 [27.0 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 1:5.11-2.1 [204 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.31-2 [247 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-7+nmu1 [905 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-i386 3.0.10-3 [20.3 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.33.12+really2.32.4-5 [1819 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.6-2 [133 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5 [440 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-i386 0.18.1.1-10 [141 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 1:5.11-2.1 [51.6 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.18.1.1-10 [131 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-i386 1.3.2a-15 [101 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev kfreebsd-i386 0.18.1.1-10 [26.6 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev kfreebsd-i386 0.18.1.1-10 [170 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.18.1.1-10 [1747 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-i386 1.55-3 [29.0 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9-10 [93.1 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9-10 [210 kB]
-Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.7.dfsg-13 [213 kB]
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
+ zlib1g-dev
+The following packages will be upgraded:
+ libncurses5 libtinfo5 ncurses-bin
+3 upgraded, 25 newly installed, 0 to remove and 63 not upgraded.
+Need to get 10.9 MB/10.9 MB of archives.
+After this operation, 30.3 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin kfreebsd-i386 5.9+20140913-1 [348 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 kfreebsd-i386 5.9+20140913-1 [282 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 kfreebsd-i386 5.9+20140913-1 [102 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.3.1-1 [27.7 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.22.2-8 [1073 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.5 [205 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.7.0.1-1 [1002 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.19.2-2 [30.8 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 1:5.19-2 [242 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.9.1+dfsg1-4 [833 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 kfreebsd-i386 3.1-2 [17.3 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.42.0-1 [2539 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.8-3 [140 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 kfreebsd-i386 1.1-1 [215 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5.2 [284 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 1:5.19-2 [58.1 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.19.2-2 [121 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.19.2-2 [1237 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev kfreebsd-i386 1.1-1 [255 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9+20140913-1 [75.9 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9+20140913-1 [176 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main tabix kfreebsd-i386 1.1-1 [198 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.8.dfsg-2 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.2 MB in 9s (1081 kB/s)
+Fetched 10.9 MB in 2s (5416 kB/s)
+(Reading database ... 10755 files and directories currently installed.)
+Preparing to unpack .../ncurses-bin_5.9+20140913-1_kfreebsd-i386.deb ...
+Unpacking ncurses-bin (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up ncurses-bin (5.9+20140913-1) ...
+(Reading database ... 10755 files and directories currently installed.)
+Preparing to unpack .../libtinfo5_5.9+20140913-1_kfreebsd-i386.deb ...
+Unpacking libtinfo5:kfreebsd-i386 (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up libtinfo5:kfreebsd-i386 (5.9+20140913-1) ...
+Processing triggers for libc-bin (2.19-9) ...
+(Reading database ... 10755 files and directories currently installed.)
+Preparing to unpack .../libncurses5_5.9+20140913-1_kfreebsd-i386.deb ...
+Unpacking libncurses5:kfreebsd-i386 (5.9+20140913-1) over (5.9+20140712-2) ...
+Setting up libncurses5:kfreebsd-i386 (5.9+20140913-1) ...
+Processing triggers for libc-bin (2.19-9) ...
Selecting previously unselected package libpipeline1:kfreebsd-i386.
-(Reading database ... 11302 files and directories currently installed.)
-Unpacking libpipeline1:kfreebsd-i386 (from .../libpipeline1_1.2.2-2_kfreebsd-i386.deb) ...
+(Reading database ... 10755 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.3.1-1_kfreebsd-i386.deb ...
+Unpacking libpipeline1:kfreebsd-i386 (1.3.1-1) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_kfreebsd-i386.deb) ...
+Preparing to unpack .../groff-base_1.22.2-8_kfreebsd-i386.deb ...
+Unpacking groff-base (1.22.2-8) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_kfreebsd-i386.deb) ...
+Preparing to unpack .../bsdmainutils_9.0.5_kfreebsd-i386.deb ...
+Unpacking bsdmainutils (9.0.5) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_kfreebsd-i386.deb) ...
+Preparing to unpack .../man-db_2.7.0.1-1_kfreebsd-i386.deb ...
+Unpacking man-db (2.7.0.1-1) ...
Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
+Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
+Unpacking bash-completion (1:2.1-4) ...
Selecting previously unselected package libasprintf0c2:kfreebsd-i386.
-Unpacking libasprintf0c2:kfreebsd-i386 (from .../libasprintf0c2_0.18.1.1-10_kfreebsd-i386.deb) ...
+Preparing to unpack .../libasprintf0c2_0.19.2-2_kfreebsd-i386.deb ...
+Unpacking libasprintf0c2:kfreebsd-i386 (0.19.2-2) ...
Selecting previously unselected package libmagic1:kfreebsd-i386.
-Unpacking libmagic1:kfreebsd-i386 (from .../libmagic1_1%3a5.11-2.1_kfreebsd-i386.deb) ...
-Selecting previously unselected package libpcre3:kfreebsd-i386.
-Unpacking libpcre3:kfreebsd-i386 (from .../libpcre3_1%3a8.31-2_kfreebsd-i386.deb) ...
+Preparing to unpack .../libmagic1_1%3a5.19-2_kfreebsd-i386.deb ...
+Unpacking libmagic1:kfreebsd-i386 (1:5.19-2) ...
Selecting previously unselected package libxml2:kfreebsd-i386.
-Unpacking libxml2:kfreebsd-i386 (from .../libxml2_2.8.0+dfsg1-7+nmu1_kfreebsd-i386.deb) ...
-Selecting previously unselected package libffi5:kfreebsd-i386.
-Unpacking libffi5:kfreebsd-i386 (from .../libffi5_3.0.10-3_kfreebsd-i386.deb) ...
+Preparing to unpack .../libxml2_2.9.1+dfsg1-4_kfreebsd-i386.deb ...
+Unpacking libxml2:kfreebsd-i386 (2.9.1+dfsg1-4) ...
+Selecting previously unselected package libffi6:kfreebsd-i386.
+Preparing to unpack .../libffi6_3.1-2_kfreebsd-i386.deb ...
+Unpacking libffi6:kfreebsd-i386 (3.1-2) ...
Selecting previously unselected package libglib2.0-0:kfreebsd-i386.
-Unpacking libglib2.0-0:kfreebsd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-5_kfreebsd-i386.deb) ...
+Preparing to unpack .../libglib2.0-0_2.42.0-1_kfreebsd-i386.deb ...
+Unpacking libglib2.0-0:kfreebsd-i386 (2.42.0-1) ...
Selecting previously unselected package libcroco3:kfreebsd-i386.
-Unpacking libcroco3:kfreebsd-i386 (from .../libcroco3_0.6.6-2_kfreebsd-i386.deb) ...
+Preparing to unpack .../libcroco3_0.6.8-3_kfreebsd-i386.deb ...
+Unpacking libcroco3:kfreebsd-i386 (0.6.8-3) ...
+Selecting previously unselected package libhts1:kfreebsd-i386.
+Preparing to unpack .../libhts1_1.1-1_kfreebsd-i386.deb ...
+Unpacking libhts1:kfreebsd-i386 (1.1-1) ...
Selecting previously unselected package libunistring0:kfreebsd-i386.
-Unpacking libunistring0:kfreebsd-i386 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
-Selecting previously unselected package libgettextpo0:kfreebsd-i386.
-Unpacking libgettextpo0:kfreebsd-i386 (from .../libgettextpo0_0.18.1.1-10_kfreebsd-i386.deb) ...
+Preparing to unpack .../libunistring0_0.9.3-5.2_kfreebsd-i386.deb ...
+Unpacking libunistring0:kfreebsd-i386 (0.9.3-5.2) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_kfreebsd-i386.deb) ...
+Preparing to unpack .../file_1%3a5.19-2_kfreebsd-i386.deb ...
+Unpacking file (1:5.19-2) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_kfreebsd-i386.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
-Selecting previously unselected package libasprintf-dev:kfreebsd-i386.
-Unpacking libasprintf-dev:kfreebsd-i386 (from .../libasprintf-dev_0.18.1.1-10_kfreebsd-i386.deb) ...
-Selecting previously unselected package libgettextpo-dev:kfreebsd-i386.
-Unpacking libgettextpo-dev:kfreebsd-i386 (from .../libgettextpo-dev_0.18.1.1-10_kfreebsd-i386.deb) ...
+Preparing to unpack .../gettext-base_0.19.2-2_kfreebsd-i386.deb ...
+Unpacking gettext-base (0.19.2-2) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_kfreebsd-i386.deb) ...
+Preparing to unpack .../gettext_0.19.2-2_kfreebsd-i386.deb ...
+Unpacking gettext (0.19.2-2) ...
Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.1) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
+Unpacking po-debconf (1.0.16+nmu3) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_kfreebsd-i386.deb) ...
+Preparing to unpack .../debhelper_9.20140817_all.deb ...
+Unpacking debhelper (9.20140817) ...
+Selecting previously unselected package libhts-dev:kfreebsd-i386.
+Preparing to unpack .../libhts-dev_1.1-1_kfreebsd-i386.deb ...
+Unpacking libhts-dev:kfreebsd-i386 (1.1-1) ...
Selecting previously unselected package libtinfo-dev:kfreebsd-i386.
-Unpacking libtinfo-dev:kfreebsd-i386 (from .../libtinfo-dev_5.9-10_kfreebsd-i386.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_kfreebsd-i386.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
+Preparing to unpack .../libtinfo-dev_5.9+20140913-1_kfreebsd-i386.deb ...
+Unpacking libtinfo-dev:kfreebsd-i386 (5.9+20140913-1) ...
+Selecting previously unselected package libncurses5-dev:kfreebsd-i386.
+Preparing to unpack .../libncurses5-dev_5.9+20140913-1_kfreebsd-i386.deb ...
+Unpacking libncurses5-dev:kfreebsd-i386 (5.9+20140913-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.1-1_kfreebsd-i386.deb ...
+Unpacking tabix (1.1-1) ...
Selecting previously unselected package zlib1g-dev:kfreebsd-i386.
-Unpacking zlib1g-dev:kfreebsd-i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_kfreebsd-i386.deb) ...
-Setting up libpipeline1:kfreebsd-i386 (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_kfreebsd-i386.deb ...
+Unpacking zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-2) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up libpipeline1:kfreebsd-i386 (1.3.1-1) ...
+Setting up groff-base (1.22.2-8) ...
+Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:kfreebsd-i386 (0.18.1.1-10) ...
-Setting up libmagic1:kfreebsd-i386 (1:5.11-2.1) ...
-Setting up libpcre3:kfreebsd-i386 (1:8.31-2) ...
-Setting up libxml2:kfreebsd-i386 (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:kfreebsd-i386 (3.0.10-3) ...
-Setting up libglib2.0-0:kfreebsd-i386 (2.33.12+really2.32.4-5) ...
+Setting up man-db (2.7.0.1-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up bash-completion (1:2.1-4) ...
+Setting up libasprintf0c2:kfreebsd-i386 (0.19.2-2) ...
+Setting up libmagic1:kfreebsd-i386 (1:5.19-2) ...
+Setting up libxml2:kfreebsd-i386 (2.9.1+dfsg1-4) ...
+Setting up libffi6:kfreebsd-i386 (3.1-2) ...
+Setting up libglib2.0-0:kfreebsd-i386 (2.42.0-1) ...
No schema files found: doing nothing.
-Setting up libcroco3:kfreebsd-i386 (0.6.6-2) ...
-Setting up libunistring0:kfreebsd-i386 (0.9.3-5) ...
-Setting up libgettextpo0:kfreebsd-i386 (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:kfreebsd-i386 (0.18.1.1-10) ...
-Setting up libgettextpo-dev:kfreebsd-i386 (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
+Setting up libcroco3:kfreebsd-i386 (0.6.8-3) ...
+Setting up libhts1:kfreebsd-i386 (1.1-1) ...
+Setting up libunistring0:kfreebsd-i386 (0.9.3-5.2) ...
+Setting up file (1:5.19-2) ...
+Setting up gettext-base (0.19.2-2) ...
+Setting up gettext (0.19.2-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:kfreebsd-i386 (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
-Checking correctness of dependencies...
-Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 kfreebsd-kernel-headers_0.83 libc0.1-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.4 [...]
+Setting up po-debconf (1.0.16+nmu3) ...
+Setting up debhelper (9.20140817) ...
+Setting up libhts-dev:kfreebsd-i386 (1.1-1) ...
+Setting up libtinfo-dev:kfreebsd-i386 (5.9+20140913-1) ...
+Setting up libncurses5-dev:kfreebsd-i386 (5.9+20140913-1) ...
+Setting up tabix (1.1-1) ...
+Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-2) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-9) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: GNU/kFreeBSD 9.0-2-686 kfreebsd-i386 (i386)
+Toolchain package versions: binutils_2.24.51.20140818-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-8 gcc-4.9_4.9.1-8 kfreebsd-kernel-headers_10.0~5 libc0.1-dev_2.19-9 libstdc++-4.9-dev_4.9.1-8 libstdc++6_4.9.1-8
+Package versions: apt_1.0.6 base-files_7.5 base-passwd_3.5.33 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140818-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.21-1.2 cpp_4:4.9.1-3 cpp-4.9_4.9.1-8 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2012.4 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.11-2 e2fsprogs_1.42.11-2 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_ [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -319,589 +327,1616 @@ Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.1
+dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying dynamic-build.patch
+dpkg-source: info: applying debian-changes
Check disc space
────────────────
+Sufficient free space for build
+
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=parallel=2
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=sid-kfreebsd-i386-sbuild
+SCHROOT_CHROOT_NAME=sid-ki-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-ki-sbuild-1411604684-24335
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
+dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.1
dpkg-buildpackage: host architecture kfreebsd-i386
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j2 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f TAGS
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_auto_configure -a -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j2 HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_kfreebsd-i386.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.19-1_kfreebsd-i386.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0919
-
-samtools_0.1.19-1_kfreebsd-i386.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: kfreebsd-i386
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 27b9febcc040764f37a46813eba6a7ad4cf0e829 563422 samtools_0.1.19-1_kfreebsd-i386.deb
- e6a74f1cd847e4b67206ba343a2f880ceaf269fd 126860 libbam-dev_0.1.19-1_kfreebsd-i386.deb
-Checksums-Sha256:
- 0728e1915c932f365f494d7561232329b2b908d090e06dc8fcd2e54fa41a7236 563422 samtools_0.1.19-1_kfreebsd-i386.deb
- 126393589b66b1279cec18a24dd5b8e58ba5ffe25d7e76baf409934ef41b2c1c 126860 libbam-dev_0.1.19-1_kfreebsd-i386.deb
-Files:
- 57b519fdea3b23c74169e55f1638881c 563422 science optional samtools_0.1.19-1_kfreebsd-i386.deb
- c94271270f5dd96bcf856e8b2f4ce86b 126860 libdevel optional libbam-dev_0.1.19-1_kfreebsd-i386.deb
+padding.c:199:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
+ fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+ ^
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+misc/ace2sam.c: In function 'main':
+misc/ace2sam.c:112:13: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=]
+ fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
+ ^
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+test/merge/test_rtrans_build.c: In function 'main':
+test/merge/test_rtrans_build.c:79:29: warning: overflow in implicit constant conversion [-Woverflow]
+ const long GIMIC_SEED = 0x1234abcd330e;
+ ^
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+test/merge/test_trans_tbl_init.c: In function 'main':
+test/merge/test_trans_tbl_init.c:323:31: warning: overflow in implicit constant conversion [-Woverflow]
+ const long GIMMICK_SEED = 0x1234abcd330e;
+ ^
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lcurs [...]
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip
+make[2]: Entering directory '/«PKGBUILDDIR»'
+REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/pJK7mljtU5/bgzip.dat.gz
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/pJK7mljtU5/bgzip.dat.gz
+.. ok
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/pJK7mljtU5/bgzip.dat.gz
+.. ok
-samtools_0.1.19-1_kfreebsd-i386.deb
-───────────────────────────────────
-
- new debian package, version 2.0.
- size 563422 bytes: control archive= 1941 bytes.
- 32 bytes, 1 lines conffiles
- 802 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: kfreebsd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1298
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: processing sequence alignments in SAM and BAM formats
- Samtools is a set of utilities that manipulate nucleotide sequence alignments
- in the binary BAM format. It imports from and exports to the ascii SAM
- (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- to retrieve reads in any regions swiftly. It is designed to work on a stream,
- and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 09:18 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2013-03-30 09:19 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 09:19 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 09:19 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:19 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/bin/
--rwxr-xr-x root/root 157732 2013-03-30 09:19 ./usr/bin/bcftools
--rwxr-xr-x root/root 26152 2013-03-30 09:19 ./usr/bin/razip
--rwxr-xr-x root/root 439700 2013-03-30 09:19 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/samtools/
--rwxr-xr-x root/root 17896 2013-03-30 09:19 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 17840 2013-03-30 09:19 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 187448 2013-03-30 09:19 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 9628 2013-03-30 09:19 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9628 2013-03-30 09:19 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13728 2013-03-30 09:19 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9604 2013-03-30 09:19 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_kfreebsd-i386.deb
-─────────────────────────────────────
-
- new debian package, version 2.0.
- size 126860 bytes: control archive= 931 bytes.
- 720 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: kfreebsd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 373
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/
--rw-r--r-- root/root 291856 2013-03-30 09:19 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/include/samtools/
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
+/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
+/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /tmp/pJK7mljtU5/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/pJK7mljtU5/large_chrom.bam ref2
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/dat/large_chrom.out
+ /«PKGBUILDDIR»/test/dat/large_chrom.out.new
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/pJK7mljtU5/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/pJK7mljtU5/mpileup.bam.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/pJK7mljtU5/mpileup.cram.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/pJK7mljtU5/mpileup.bam.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/pJK7mljtU5/mpileup.cram.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/pJK7mljtU5/mpileup.cram.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/pJK7mljtU5/mpileup.cram.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/pJK7mljtU5/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/pJK7mljtU5/mpileup.1.cram | grep -v mpileup
+test/test.pl: module IO::Pty not found; skipping usage tests
+.. ok
+
+test_usage:
+ samtools
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM
+ SAM files differ at /tmp/pJK7mljtU5/view.test001.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test001.bam -b /tmp/pJK7mljtU5/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test001.bam.sam /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 2: SAM -> uncompressed BAM .. ok
+
+ 3: uncompressed BAM -> SAM and compare
+ SAM files differ at /tmp/pJK7mljtU5/view.test003.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test003.sam -h /tmp/pJK7mljtU5/view.test002.bam
+
+
+.. failed ...
+
+ 4: SAM -> fast compressed BAM .. ok
+
+ 5: fast compressed BAM -> SAM and compare
+ SAM files differ at /tmp/pJK7mljtU5/view.test005.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test005.sam -h /tmp/pJK7mljtU5/view.test004.bam
+
+
+.. failed ...
+
+ 6: SAM -> CRAM -> SAM (UR header tags)
+ SAM files differ at /tmp/pJK7mljtU5/view.test006.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test006.cram -C /tmp/pJK7mljtU5/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test006.cram.sam /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 7: SAM -> CRAM -> SAM (M5 header tags)
+ SAM files differ at /tmp/pJK7mljtU5/view.test007.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test007.cram -C /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test007.cram.sam /tmp/pJK7mljtU5/view.test007.cram
+
+
+.. failed ...
+
+ 8: BAM -> CRAM with UR -> SAM
+ SAM files differ at /tmp/pJK7mljtU5/view.test008.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test008.cram -C /tmp/pJK7mljtU5/view.test001.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test008.cram.sam /tmp/pJK7mljtU5/view.test008.cram
+
+
+.. failed ...
+
+ 9: SAM -> BAM (M5 header tags)
+ SAM files differ at /tmp/pJK7mljtU5/view.test009.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test009.bam -b /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test009.bam.sam /tmp/pJK7mljtU5/view.test009.bam
+
+
+.. failed ...
+
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags)
+ SAM files differ at /tmp/pJK7mljtU5/view.test010.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test010.cram -C /tmp/pJK7mljtU5/view.test009.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test010.cram.sam /tmp/pJK7mljtU5/view.test010.cram
+
+
+.. failed ...
+
+ 11: CRAM -> BAM with UR
+ SAM files differ at /tmp/pJK7mljtU5/view.test011.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test011.bam -b /tmp/pJK7mljtU5/view.test008.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test011.bam.sam /tmp/pJK7mljtU5/view.test011.bam
+
+
+.. failed ...
+
+ 12: CRAM -> BAM with M5
+ SAM files differ at /tmp/pJK7mljtU5/view.test012.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test012.bam -b /tmp/pJK7mljtU5/view.test010.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test012.bam.sam /tmp/pJK7mljtU5/view.test012.bam
+
+
+.. failed ...
+
+ 13: SAM -> SAM via stdout
+ SAM files differ at /tmp/pJK7mljtU5/view.test013.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -h /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 14: SAM -> BAM via stdout .. ok
+
+ 15: SAM -> CRAM via stdout
+ SAM files differ at /tmp/pJK7mljtU5/view.test015.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -C /tmp/pJK7mljtU5/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test015.cram.sam /tmp/pJK7mljtU5/view.test015.cram
+
+
+.. failed ...
+
+ 16: SAM from stdin -> SAM
+ SAM files differ at /tmp/pJK7mljtU5/view.test016.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test016.sam -h -
+
+
+.. failed ...
+
+ 17: BAM from stdin -> SAM
+ SAM files differ at /tmp/pJK7mljtU5/view.test017.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test017.sam -h -
+
+
+.. failed ...
+
+ 18: CRAM from stdin -> SAM
+ SAM files differ at /tmp/pJK7mljtU5/view.test018.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test018.sam -h -
+
+
+.. failed ...
+
+ 19: samtools view -H (SAM input) .. ok
+
+ 20: samtools view -H (BAM input) .. ok
+
+ 21: samtools view -H (CRAM input) .. ok
+
+ 22: No headers (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test022.body : 6 / /tmp/pJK7mljtU5/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test022.body /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 23: No headers (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test023.body : 6 / /tmp/pJK7mljtU5/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test023.body /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 24: No headers (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test024.body : 6 / /tmp/pJK7mljtU5/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test024.body /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 25: Filter -f 128 (SAM input) .. ok
+
+ 26: Count -f 128 (SAM input) .. ok
+
+ 27: Filter -f 128 (BAM input) .. ok
+
+ 28: Count -f 128 (BAM input) .. ok
+
+ 29: Filter -f 128 (CRAM input) .. ok
+
+ 30: Count -f 128 (CRAM input) .. ok
+
+ 31: Filter -F 128 (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test031.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test031.sam -h -F 128 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 32: Count -F 128 (SAM input) .. ok
+
+ 33: Filter -F 128 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test033.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test033.sam -h -F 128 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 34: Count -F 128 (BAM input) .. ok
+
+ 35: Filter -F 128 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test035.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test035.sam -h -F 128 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 36: Count -F 128 (CRAM input) .. ok
+
+ 37: Filter -F 128 -f 2 (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test037.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test037.sam -h -F 128 -f 2 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 38: Count -F 128 -f 2 (SAM input) .. ok
+
+ 39: Filter -F 128 -f 2 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test039.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test039.sam -h -F 128 -f 2 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 40: Count -F 128 -f 2 (BAM input) .. ok
+
+ 41: Filter -F 128 -f 2 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test041.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test041.sam -h -F 128 -f 2 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 42: Count -F 128 -f 2 (CRAM input) .. ok
+
+ 43: Filter -r grp2 (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test043.sam : 29 / /tmp/pJK7mljtU5/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test043.sam -h -r grp2 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 44: Count -r grp2 (SAM input) .. ok
+
+ 45: Filter -r grp2 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test045.sam : 29 / /tmp/pJK7mljtU5/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test045.sam -h -r grp2 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 46: Count -r grp2 (BAM input) .. ok
+
+ 47: Filter -r grp2 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test047.sam : 29 / /tmp/pJK7mljtU5/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test047.sam -h -r grp2 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 48: Count -r grp2 (CRAM input) .. ok
+
+ 49: Filter -R /tmp/pJK7mljtU5/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/pJK7mljtU5/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/pJK7mljtU5/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/pJK7mljtU5/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/pJK7mljtU5/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/pJK7mljtU5/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test055.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test055.sam -h -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 56: Count -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test057.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test057.sam -h -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 58: Count -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test059.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test059.sam -h -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 60: Count -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test061.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test061.sam -h -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 62: Count -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test063.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test063.sam -h -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 64: Count -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test065.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test065.sam -h -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 66: Count -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (CRAM input).. ok
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 67: Filter -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test067.sam -h -l Library 2 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 68: Count -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 69: Filter -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test069.sam -h -l Library 2 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 70: Count -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 71: Filter -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test071.sam -h -l Library 2 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 72: Count -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. expected failure
+
+ 73: Filter -q 50 (SAM input) .. ok
+
+ 74: Count -q 50 (SAM input) .. ok
+
+ 75: Filter -q 50 (BAM input) .. ok
+
+ 76: Count -q 50 (BAM input) .. ok
+
+ 77: Filter -q 50 (CRAM input) .. ok
+
+ 78: Count -q 50 (CRAM input) .. ok
+
+ 79: Filter -q 99 (SAM input) .. ok
+
+ 80: Count -q 99 (SAM input) .. ok
+
+ 81: Filter -q 99 (BAM input) .. ok
+
+ 82: Count -q 99 (BAM input) .. ok
+
+ 83: Filter -q 99 (CRAM input) .. ok
+
+ 84: Count -q 99 (CRAM input) .. ok
+
+ 85: Filter -q 100 (SAM input) .. ok
+
+ 86: Count -q 100 (SAM input) .. ok
+
+ 87: Filter -q 100 (BAM input) .. ok
+
+ 88: Count -q 100 (BAM input) .. ok
+
+ 89: Filter -q 100 (CRAM input) .. ok
+
+ 90: Count -q 100 (CRAM input) .. ok
+
+ 91: Filter -x fa (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test091.sam : 34 / /tmp/pJK7mljtU5/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test091.sam -h -x fa /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 92: Count -x fa (SAM input) .. ok
+
+ 93: Filter -x fa (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test093.sam : 34 / /tmp/pJK7mljtU5/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test093.sam -h -x fa /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 94: Count -x fa (BAM input) .. ok
+
+ 95: Filter -x fa (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test095.sam : 34 / /tmp/pJK7mljtU5/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test095.sam -h -x fa /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 96: Count -x fa (CRAM input) .. ok
+
+ 97: Filter -x fa -x ha (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test097.sam : 34 / /tmp/pJK7mljtU5/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test097.sam -h -x fa -x ha /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 98: Count -x fa -x ha (SAM input) .. ok
+
+ 99: Filter -x fa -x ha (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test099.sam : 34 / /tmp/pJK7mljtU5/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test099.sam -h -x fa -x ha /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 100: Count -x fa -x ha (BAM input) .. ok
+
+ 101: Filter -x fa -x ha (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test101.sam : 34 / /tmp/pJK7mljtU5/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test101.sam -h -x fa -x ha /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 102: Count -x fa -x ha (CRAM input) .. ok
+
+ 103: Filter -x fa -r grp2 (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test103.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test103.sam -h -x fa -r grp2 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 104: Count -x fa -r grp2 (SAM input) .. ok
+
+ 105: Filter -x fa -r grp2 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test105.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test105.sam -h -x fa -r grp2 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 106: Count -x fa -r grp2 (BAM input) .. ok
+
+ 107: Filter -x fa -r grp2 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test107.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test107.sam -h -x fa -r grp2 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 108: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 109: Filter -x RG -r grp2 (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test109.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test109.sam -h -x RG -r grp2 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 110: Count -x RG -r grp2 (SAM input) .. ok
+
+ 111: Filter -x RG -r grp2 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test111.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test111.sam -h -x RG -r grp2 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 112: Count -x RG -r grp2 (BAM input) .. ok
+
+ 113: Filter -x RG -r grp2 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test113.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test113.sam -h -x RG -r grp2 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 114: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 115: Filter -m 10 (SAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test115.sam : 34 / /tmp/pJK7mljtU5/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test115.sam -h -m 10 /tmp/pJK7mljtU5/view.001.sam
+
+
+.. failed ...
+
+ 116: Count -m 10 (SAM input) .. ok
+
+ 117: Filter -m 10 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test117.sam : 34 / /tmp/pJK7mljtU5/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test117.sam -h -m 10 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 118: Count -m 10 (BAM input) .. ok
+
+ 119: Filter -m 10 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test119.sam : 34 / /tmp/pJK7mljtU5/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test119.sam -h -m 10 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 120: Count -m 10 (CRAM input) .. ok
+
+ 121: Filter -m 11 (SAM input) .. ok
+
+ 122: Count -m 11 (SAM input) .. ok
+
+ 123: Filter -m 11 (BAM input) .. ok
+
+ 124: Count -m 11 (BAM input) .. ok
+
+ 125: Filter -m 11 (CRAM input) .. ok
+
+ 126: Count -m 11 (CRAM input) .. ok
+
+ 127: Filter -m 15 (SAM input) .. ok
+
+ 128: Count -m 15 (SAM input) .. ok
+
+ 129: Filter -m 15 (BAM input) .. ok
+
+ 130: Count -m 15 (BAM input) .. ok
+
+ 131: Filter -m 15 (CRAM input) .. ok
+
+ 132: Count -m 15 (CRAM input) .. ok
+
+ 133: Filter -m 16 (SAM input) .. ok
+
+ 134: Count -m 16 (SAM input) .. ok
+
+ 135: Filter -m 16 (BAM input) .. ok
+
+ 136: Count -m 16 (BAM input) .. ok
+
+ 137: Filter -m 16 (CRAM input) .. ok
+
+ 138: Count -m 16 (CRAM input) .. ok
+
+ 139: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 140: Region Z (BAM input) .. ok
+
+ 141: Count Z (BAM input) .. ok
+
+ 142: Region Z (CRAM input) .. ok
+
+ 143: Count Z (CRAM input) .. ok
+
+ 144: Region Z:30 (BAM input) .. ok
+
+ 145: Count Z:30 (BAM input) .. ok
+
+ 146: Region Z:30 (CRAM input) .. ok
+
+ 147: Count Z:30 (CRAM input) .. ok
+
+ 148: Region Z:20-40 (BAM input) .. ok
+
+ 149: Count Z:20-40 (BAM input) .. ok
+
+ 150: Region Z:20-40 (CRAM input) .. ok
+
+ 151: Count Z:20-40 (CRAM input) .. ok
+
+ 152: Region ref1 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test152.sam : 34 / /tmp/pJK7mljtU5/view.reg1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test152.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1
+
+
+.. failed ...
+
+ 153: Count ref1 (BAM input) .. ok
+
+ 154: Region ref1 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test154.sam : 34 / /tmp/pJK7mljtU5/view.reg1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test154.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1
+
+
+.. failed ...
+
+ 155: Count ref1 (CRAM input) .. ok
+
+ 156: Region ref1:15 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test156.sam : 31 / /tmp/pJK7mljtU5/view.reg2.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test156.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15
+
+
+.. failed ...
+
+ 157: Count ref1:15 (BAM input) .. ok
+
+ 158: Region ref1:15 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test158.sam : 31 / /tmp/pJK7mljtU5/view.reg2.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test158.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15
+
+
+.. failed ...
+
+ 159: Count ref1:15 (CRAM input) .. ok
+
+ 160: Region ref1:15-45 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test160.sam : 31 / /tmp/pJK7mljtU5/view.reg3.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test160.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-45
+
+
+.. failed ...
+
+ 161: Count ref1:15-45 (BAM input) .. ok
+
+ 162: Region ref1:15-45 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test162.sam : 31 / /tmp/pJK7mljtU5/view.reg3.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test162.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-45
+
+
+.. failed ...
+
+ 163: Count ref1:15-45 (CRAM input) .. ok
+
+ 164: Region ref1:15-45 ref2 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test164.sam : 31 / /tmp/pJK7mljtU5/view.reg4.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test164.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-45 ref2
+
+
+.. failed ...
+
+ 165: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 166: Region ref1:15-45 ref2 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test166.sam : 31 / /tmp/pJK7mljtU5/view.reg4.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test166.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-45 ref2
+
+
+.. failed ...
+
+ 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 168: Region ref1:15-45 ref2:16 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test168.sam : 31 / /tmp/pJK7mljtU5/view.reg5.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test168.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-45 ref2:16
+
+
+.. failed ...
+
+ 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 170: Region ref1:15-45 ref2:16 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test170.sam : 31 / /tmp/pJK7mljtU5/view.reg5.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test170.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-45 ref2:16
+
+
+.. failed ...
+
+ 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 172: Region ref1:15-45 ref2:16-31 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test172.sam : 31 / /tmp/pJK7mljtU5/view.reg6.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test172.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-45 ref2:16-31
+
+
+.. failed ...
+
+ 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test174.sam : 31 / /tmp/pJK7mljtU5/view.reg6.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test174.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-45 ref2:16-31
+
+
+.. failed ...
+
+ 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 176: Region ref1:15-15 ref1:45-45 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test176.sam : 31 / /tmp/pJK7mljtU5/view.reg7.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test176.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-15 ref1:45-45
+
+
+.. failed ...
+
+ 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test178.sam : 31 / /tmp/pJK7mljtU5/view.reg7.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test178.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-15 ref1:45-45
+
+
+.. failed ...
+
+ 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 180: Region -f 128 ref1 (BAM input) .. ok
+
+ 181: Count -f 128 ref1 (BAM input) .. ok
+
+ 182: Region -f 128 ref1 (CRAM input) .. ok
+
+ 183: Count -f 128 ref1 (CRAM input) .. ok
+
+ 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 188: Region -r grp2 ref1:15-45 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test188.sam : 28 / /tmp/pJK7mljtU5/view.reg10.sam : 28
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test188.sam -h -r grp2 /tmp/pJK7mljtU5/view.test001.bam ref1:15-45
+
+
+.. failed ...
+
+ 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 190: Region -r grp2 ref1:15-45 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test190.sam : 28 / /tmp/pJK7mljtU5/view.reg10.sam : 28
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test190.sam -h -r grp2 /tmp/pJK7mljtU5/view.test006.cram ref1:15-45
+
+
+.. failed ...
+
+ 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test200.sam : 33 / /tmp/pJK7mljtU5/view.bed1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test200.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test202.sam : 33 / /tmp/pJK7mljtU5/view.bed1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test202.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test204.sam : 34 / /tmp/pJK7mljtU5/view.bed2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test204.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test206.sam : 34 / /tmp/pJK7mljtU5/view.bed2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test206.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test224.sam : 33 / /tmp/pJK7mljtU5/view.bed1r1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test224.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/pJK7mljtU5/view.test001.bam ref1:11-16
+
+
+.. failed ...
+
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test226.sam : 33 / /tmp/pJK7mljtU5/view.bed1r1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test226.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/pJK7mljtU5/view.test006.cram ref1:11-16
+
+
+.. failed ...
+
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test240.sam : 29 / /tmp/pJK7mljtU5/view.bed1f3.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test240.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/pJK7mljtU5/view.test001.bam
+
+
+.. failed ...
+
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input)
+ SAM files differ at /tmp/pJK7mljtU5/view.test242.sam : 29 / /tmp/pJK7mljtU5/view.bed1f3.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test242.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/pJK7mljtU5/view.test006.cram
+
+
+.. failed ...
+
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 248: Make BAM with no M5/UR tags
+ SAM files differ at /tmp/pJK7mljtU5/view.001.no_sq.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.001.no_sq.bam -b /tmp/pJK7mljtU5/view.001.no_m5.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.001.no_sq.bam.sam /tmp/pJK7mljtU5/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 249: Add @SQ with -t (SAM -> SAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test249.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test249.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.sam
+
+
+.. failed ...
+
+ 250: Add @SQ with -T (SAM -> SAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test250.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test250.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.sam
+
+
+.. failed ...
+
+ 251: Add @SQ with -t (BAM -> SAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test251.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test251.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 252: Add @SQ with -T (BAM -> SAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test252.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test252.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 253: Add @SQ with -t (SAM -> BAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test253.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test253.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test253.bam.sam /tmp/pJK7mljtU5/view.test253.bam
+
+
+.. failed ...
+
+ 254: Add @SQ with -T (SAM -> BAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test254.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test254.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test254.bam.sam /tmp/pJK7mljtU5/view.test254.bam
+
+
+.. failed ...
+
+ 255: Add @SQ with -t (BAM -> BAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test255.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test255.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test255.bam.sam /tmp/pJK7mljtU5/view.test255.bam
+
+
+.. failed ...
+
+ 256: Add @SQ with -T (BAM -> BAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test256.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test256.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test256.bam.sam /tmp/pJK7mljtU5/view.test256.bam
+
+
+.. failed ...
+
+ 257: Add @SQ with -t (SAM -> CRAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test257.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test257.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test257.cram.sam /tmp/pJK7mljtU5/view.test257.cram
+
+
+.. failed ...
+
+ 258: Add @SQ with -T (SAM -> CRAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test258.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test258.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test258.cram.sam /tmp/pJK7mljtU5/view.test258.cram
+
+
+.. failed ...
+
+ 259: Add @SQ with -t (BAM -> CRAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test259.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test259.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test259.cram.sam /tmp/pJK7mljtU5/view.test259.cram
+
+
+.. failed ...
+
+ 260: Add @SQ with -T (BAM -> CRAM)
+ SAM files differ at /tmp/pJK7mljtU5/view.test260.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test260.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test260.cram.sam /tmp/pJK7mljtU5/view.test260.cram
+
+
+.. failed ...
+
+ 261: CIGAR B-operator removal .. ok
+
+ 262: Big SAM -> BAM .. ok
+
+ 263: Big SAM -> BAM (2 threads) .. ok
+
+ 264: Big SAM -> BAM (4 threads) .. ok
+
+ 265: Big SAM -> CRAM .. ok
+
+ 266: Big SAM -> CRAM (2 threads) .. ok
+
+ 267: Big SAM -> CRAM (4 threads) .. ok
+
+ 268: Subsample 0.2 (SAM input) ............ ok
+
+ 269: Subsample 0.5 (SAM input) ............ ok
+
+ 270: Subsample 0.8 (SAM input) ............ ok
+
+ 271: Subsample 0.2 (BAM input) ............ ok
+
+ 272: Subsample 0.5 (BAM input) ............ ok
+
+ 273: Subsample 0.8 (BAM input) ............ ok
+
+ 274: Subsample 0.2 (CRAM input) ............ ok
+
+ 275: Subsample 0.5 (CRAM input) ............ ok
+
+ 276: Subsample 0.8 (CRAM input) ............ ok
+
+test_cat:
+ Generating test data file .................. done
+ Generate BAM file #1 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #2 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #3 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #4 .. ok
+
+ 1: cat BAM files .. ok
+
+ 2: cat recompressed BAM files .. ok
+
+ 3: cat BAM files to stdout .. ok
+
+ 4: cat recompressed BAM files to stdout .. ok
+
+ 5: cat BAM files with new header .. ok
+
+ 6: cat recompressed BAM files with new header .. ok
+
+test_bam2fq:
+ Generate BAM file
+ SAM files differ at GLOB(0x84f07d8) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/bam2fq.001.bam -b /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/pJK7mljtU5/bam2fq.001.bam
+
+
+.. failed ...
+
+ Generate CRAM file
+ SAM files differ at GLOB(0x85ff1a8) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/bam2fq.001.cram -C /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/pJK7mljtU5/bam2fq.001.cram
+
+
+.. failed ...
+
+[M::main_bam2fq] processed 36 reads
+ 1: bam2fq (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 2: bam2fq -n (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 3: bam2fq (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 4: bam2fq -n (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 5: bam2fq (CRAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 6: bam2fq -n (CRAM input) .. ok
+
+test_depad:
+ Generate BAM file .. ok
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/pJK7mljtU5/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/pJK7mljtU5/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/pJK7mljtU5/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/pJK7mljtU5/depad.001p.bam
+
+
+.. expected failure
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+/bin/bash: line 1: 41286 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/DcqMtJB7dl
+
+.. expected failure
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/V7O4LqEkef - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+
+.. expected failure
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/2_isize_overflow.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/3_reverse_read_pp_lt.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/4_reverse_read_pp_equal.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/5_ct.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
+.. ok
+
+test_idxstat:
+ /«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+
+Number of tests:
+ total .. 342
+ passed .. 237
+ failed .. 87
+ expected failure .. 18
+ unexpected pass .. 0
+
+Makefile:183: recipe for target 'test' failed
+make[2]: *** [test] Error 1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+dh_auto_test: make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip returned exit code 2
+debian/rules:18: recipe for target 'override_dh_auto_test' failed
+make[1]: *** [override_dh_auto_test] Error 2
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+debian/rules:6: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20140925-0034
+
+Finished
+────────
+
+E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
+│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1364634959-29231/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM
+Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Architecture: kfreebsd-i386
-Build-Space: 13164
-Build-Time: 75
+Build Architecture: kfreebsd-i386
+Build-Space: 20484
+Build-Time: 297
Distribution: sid
-Install-Time: 34
-Job: samtools_0.1.19-1
+Fail-Stage: build
+Host Architecture: kfreebsd-i386
+Install-Time: 112
+Job: samtools_1.1-1
+Machine Architecture: kfreebsd-i386
Package: samtools
-Package-Time: 199
-Source-Version: 0.1.19-1
-Space: 13164
-Status: successful
-Version: 0.1.19-1
+Package-Time: 586
+Source-Version: 1.1-1
+Space: 20484
+Status: attempted
+Version: 1.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0919
-Build needed 00:03:19, 13164k disc space
-Signature with key 'B31C365A' requested:
+Finished at 20140925-0034
+Build needed 00:09:46, 20484k disc space
diff --git a/mipsel.log b/mipsel.log
index 0adf0e4..265c1be 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,58 +1,74 @@
-From buildd at mayer.debian.org Sat Mar 30 09:25:04 2013
-Return-path: <buildd at mayer.debian.org>
-Received: from muffat.debian.org ([206.12.19.146])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1ULs22-0003vN-UH
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:25:03 +0000
-Received: from mayer.debian.org ([140.211.166.78])
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- by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
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-Date: Sat, 30 Mar 2013 09:24:57 +0000
-Message-Id: <E1ULs1x-0005a0-Te at mayer.debian.org>
-From: buildd on mayer <buildd at mayer.debian.org>
+From buildd at eysler.debian.org Thu Sep 25 02:28:22 2014
+Return-path: <buildd at eysler.debian.org>
+Received: from mailly.debian.org ([2001:41b8:202:deb:6564:a62:52c3:4b72])
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+ CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
+ by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
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+ CN=eysler.debian.org, EMAIL=hostmaster at eysler.debian.org (verified)
+ by mailly.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at eysler.debian.org>)
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+ for logs at buildd.debian.org; Thu, 25 Sep 2014 02:28:18 +0000
+Content-Transfer-Encoding: binary
+MIME-Version: 1.0
+X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
+Date: Thu, 25 Sep 2014 02:28:17 +0000
+From: buildd on eysler <buildd at eysler.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on mipsel (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
+Subject: Log for attempted build of samtools_1.1-1 on mipsel (dist=sid)
+Key-Id: F6A5E741
+Message-Id: <E1XWyn4-0002Hb-Io at eysler.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.64.0 (17 May 2013) on eysler.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (mipsel) 30 Mar 2013 09:16 ║
+║ samtools 1.1-1 (mipsel) 25 Sep 2014 02:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: mipsel
-Hit http://debian.oregonstate.edu sid Release.gpg
-Hit http://debian.oregonstate.edu sid Release
-Get:1 http://incoming.debian.org sid Release.gpg [836 B]
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Hit http://debian.oregonstate.edu sid/main Sources
-Hit http://debian.oregonstate.edu sid/contrib Sources
-Hit http://debian.oregonstate.edu sid/main mipsel Packages
-Get:3 http://incoming.debian.org sid Release [235 kB]
-Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
-Get:4 http://incoming.debian.org Release [1141 B]
-Get:5 http://incoming.debian.org sid/main Sources [6484 kB]
-Get:6 http://incoming.debian.org sid/contrib Sources [51.0 kB]
-Get:7 http://incoming.debian.org sid/main mipsel Packages [6075 kB]
-Get:8 http://incoming.debian.org sid/contrib mipsel Packages [36.1 kB]
-Get:9 http://incoming.debian.org Sources [12.5 kB]
-Get:10 http://incoming.debian.org Packages [98.1 kB]
-Fetched 13.0 MB in 38s (334 kB/s)
+Version: 1.1-1
+Source Version: 1.1-1
+Distribution: sid
+Machine Architecture: mipsel
+Host Architecture: mipsel
+Build Architecture: mipsel
+
+I: NOTICE: Log filtering will replace 'build/samtools-WhGDgZ/samtools-1.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-WhGDgZ' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mipsel-sbuild-9da2abb3-05c8-4f5b-adf5-e24ce4b9aa67' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://ftp.at.debian.org unstable InRelease [233 kB]
+Get:2 http://ftp.debian.org unstable InRelease [233 kB]
+Get:3 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:4 http://ftp.at.debian.org unstable/main Sources [7548 kB]
+Get:5 http://incoming.debian.org buildd-unstable/main Sources [357 kB]
+Get:6 http://ftp.debian.org unstable/main Sources [7548 kB]
+Get:7 http://incoming.debian.org buildd-unstable/contrib Sources [776 B]
+Get:8 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
+Get:9 http://incoming.debian.org buildd-unstable/main mipsel Packages [282 kB]
+Get:10 http://incoming.debian.org buildd-unstable/contrib mipsel Packages [556 B]
+Get:11 http://ftp.at.debian.org unstable/contrib Sources [57.1 kB]
+Get:12 http://ftp.at.debian.org unstable/non-free Sources [107 kB]
+Get:13 http://ftp.at.debian.org unstable/main mipsel Packages [6816 kB]
+Get:14 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
+Get:15 http://ftp.debian.org unstable/non-free Sources [107 kB]
+Get:16 http://ftp.debian.org unstable/main mipsel Packages [6816 kB]
+Get:17 http://ftp.at.debian.org unstable/contrib mipsel Packages [40.6 kB]
+Get:18 http://ftp.debian.org unstable/contrib mipsel Packages [40.6 kB]
+Fetched 30.4 MB in 1min 14s (405 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -73,211 +89,208 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (449 kB/s)
+Need to get 4333 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
+Fetched 4333 kB in 1s (2765 kB/s)
Download complete and in download only mode
Check arch
──────────
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-FlpToU/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
+│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
+Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Removing negative dependencies:
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
+Need to get 0 B/816 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ... 10557 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-2j5g5j/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
+│ Install samtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.20-3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.10)
-e2fsprogs: already installed (1.42.5-1.1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
+Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ bash-completion debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
+ dh-make gettext-doc groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
+ libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 2 not upgraded.
-Need to get 193 kB/9997 kB of archives.
-After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://debian.oregonstate.edu/debian/ sid/main bash-completion all 1:2.0-1 [193 kB]
+ bash-completion debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
+ zlib1g-dev
+0 upgraded, 24 newly installed, 0 to remove and 1 not upgraded.
+Need to get 9511 kB/9512 kB of archives.
+After this operation, 30.5 MB of additional disk space will be used.
+Get:1 http://ftp.at.debian.org/debian/ unstable/main libpipeline1 mipsel 1.3.1-1 [23.5 kB]
+Get:2 http://ftp.at.debian.org/debian/ unstable/main groff-base mipsel 1.22.2-8 [1147 kB]
+Get:3 http://ftp.at.debian.org/debian/ unstable/main man-db mipsel 2.7.0.1-1 [981 kB]
+Get:4 http://ftp.at.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
+Get:5 http://ftp.at.debian.org/debian/ unstable/main libasprintf0c2 mipsel 0.19.2-2 [30.7 kB]
+Get:6 http://ftp.at.debian.org/debian/ unstable/main libmagic1 mipsel 1:5.19-2 [237 kB]
+Get:7 http://ftp.at.debian.org/debian/ unstable/main libxml2 mipsel 2.9.1+dfsg1-4 [710 kB]
+Get:8 http://ftp.at.debian.org/debian/ unstable/main libffi6 mipsel 3.1-2 [17.9 kB]
+Get:9 http://ftp.at.debian.org/debian/ unstable/main libglib2.0-0 mipsel 2.42.0-1 [2300 kB]
+Get:10 http://ftp.at.debian.org/debian/ unstable/main libcroco3 mipsel 0.6.8-3 [119 kB]
+Get:11 http://ftp.at.debian.org/debian/ unstable/main libhts1 mipsel 1.1-1 [185 kB]
+Get:12 http://ftp.at.debian.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5.2 [260 kB]
+Get:13 http://ftp.at.debian.org/debian/ unstable/main file mipsel 1:5.19-2 [58.0 kB]
+Get:14 http://ftp.at.debian.org/debian/ unstable/main gettext-base mipsel 0.19.2-2 [119 kB]
+Get:15 http://ftp.at.debian.org/debian/ unstable/main gettext mipsel 0.19.2-2 [1181 kB]
+Get:16 http://ftp.at.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://ftp.at.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
+Get:18 http://ftp.at.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
+Get:19 http://ftp.at.debian.org/debian/ unstable/main libhts-dev mipsel 1.1-1 [259 kB]
+Get:20 http://ftp.at.debian.org/debian/ unstable/main libtinfo-dev mipsel 5.9+20140913-1 [77.0 kB]
+Get:21 http://ftp.at.debian.org/debian/ unstable/main libncurses5-dev mipsel 5.9+20140913-1 [173 kB]
+Get:22 http://ftp.at.debian.org/debian/ unstable/main tabix mipsel 1.1-1 [184 kB]
+Get:23 http://ftp.at.debian.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.8.dfsg-2 [204 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 193 kB in 0s (2393 kB/s)
+Fetched 9511 kB in 3s (2481 kB/s)
Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10900 files and directories currently installed.)
-Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-2_mipsel.deb) ...
+(Reading database ... 10557 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.3.1-1_mipsel.deb ...
+Unpacking libpipeline1:mipsel (1.3.1-1) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_mipsel.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_mipsel.deb) ...
+Preparing to unpack .../groff-base_1.22.2-8_mipsel.deb ...
+Unpacking groff-base (1.22.2-8) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_mipsel.deb) ...
+Preparing to unpack .../man-db_2.7.0.1-1_mipsel.deb ...
+Unpacking man-db (2.7.0.1-1) ...
Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
+Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
+Unpacking bash-completion (1:2.1-4) ...
Selecting previously unselected package libasprintf0c2:mipsel.
-Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-10_mipsel.deb) ...
+Preparing to unpack .../libasprintf0c2_0.19.2-2_mipsel.deb ...
+Unpacking libasprintf0c2:mipsel (0.19.2-2) ...
Selecting previously unselected package libmagic1:mipsel.
-Unpacking libmagic1:mipsel (from .../libmagic1_1%3a5.11-2.1_mipsel.deb) ...
-Selecting previously unselected package libpcre3:mipsel.
-Unpacking libpcre3:mipsel (from .../libpcre3_1%3a8.31-2_mipsel.deb) ...
+Preparing to unpack .../libmagic1_1%3a5.19-2_mipsel.deb ...
+Unpacking libmagic1:mipsel (1:5.19-2) ...
Selecting previously unselected package libxml2:mipsel.
-Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-7+nmu1_mipsel.deb) ...
-Selecting previously unselected package libffi5:mipsel.
-Unpacking libffi5:mipsel (from .../libffi5_3.0.10-3_mipsel.deb) ...
+Preparing to unpack .../libxml2_2.9.1+dfsg1-4_mipsel.deb ...
+Unpacking libxml2:mipsel (2.9.1+dfsg1-4) ...
+Selecting previously unselected package libffi6:mipsel.
+Preparing to unpack .../libffi6_3.1-2_mipsel.deb ...
+Unpacking libffi6:mipsel (3.1-2) ...
Selecting previously unselected package libglib2.0-0:mipsel.
-Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.33.12+really2.32.4-5_mipsel.deb) ...
+Preparing to unpack .../libglib2.0-0_2.42.0-1_mipsel.deb ...
+Unpacking libglib2.0-0:mipsel (2.42.0-1) ...
Selecting previously unselected package libcroco3:mipsel.
-Unpacking libcroco3:mipsel (from .../libcroco3_0.6.6-2_mipsel.deb) ...
+Preparing to unpack .../libcroco3_0.6.8-3_mipsel.deb ...
+Unpacking libcroco3:mipsel (0.6.8-3) ...
+Selecting previously unselected package libhts1:mipsel.
+Preparing to unpack .../libhts1_1.1-1_mipsel.deb ...
+Unpacking libhts1:mipsel (1.1-1) ...
Selecting previously unselected package libunistring0:mipsel.
-Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
-Selecting previously unselected package libgettextpo0:mipsel.
-Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-10_mipsel.deb) ...
+Preparing to unpack .../libunistring0_0.9.3-5.2_mipsel.deb ...
+Unpacking libunistring0:mipsel (0.9.3-5.2) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_mipsel.deb) ...
+Preparing to unpack .../file_1%3a5.19-2_mipsel.deb ...
+Unpacking file (1:5.19-2) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mipsel.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
-Selecting previously unselected package libasprintf-dev:mipsel.
-Unpacking libasprintf-dev:mipsel (from .../libasprintf-dev_0.18.1.1-10_mipsel.deb) ...
-Selecting previously unselected package libgettextpo-dev:mipsel.
-Unpacking libgettextpo-dev:mipsel (from .../libgettextpo-dev_0.18.1.1-10_mipsel.deb) ...
+Preparing to unpack .../gettext-base_0.19.2-2_mipsel.deb ...
+Unpacking gettext-base (0.19.2-2) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_mipsel.deb) ...
+Preparing to unpack .../gettext_0.19.2-2_mipsel.deb ...
+Unpacking gettext (0.19.2-2) ...
Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.1) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
+Unpacking po-debconf (1.0.16+nmu3) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_mipsel.deb) ...
+Preparing to unpack .../debhelper_9.20140817_all.deb ...
+Unpacking debhelper (9.20140817) ...
+Selecting previously unselected package libhts-dev:mipsel.
+Preparing to unpack .../libhts-dev_1.1-1_mipsel.deb ...
+Unpacking libhts-dev:mipsel (1.1-1) ...
Selecting previously unselected package libtinfo-dev:mipsel.
-Unpacking libtinfo-dev:mipsel (from .../libtinfo-dev_5.9-10_mipsel.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_mipsel.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
+Preparing to unpack .../libtinfo-dev_5.9+20140913-1_mipsel.deb ...
+Unpacking libtinfo-dev:mipsel (5.9+20140913-1) ...
+Selecting previously unselected package libncurses5-dev:mipsel.
+Preparing to unpack .../libncurses5-dev_5.9+20140913-1_mipsel.deb ...
+Unpacking libncurses5-dev:mipsel (5.9+20140913-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.1-1_mipsel.deb ...
+Unpacking tabix (1.1-1) ...
Selecting previously unselected package zlib1g-dev:mipsel.
-Unpacking zlib1g-dev:mipsel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mipsel.deb) ...
-Setting up libpipeline1:mipsel (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:mipsel (0.18.1.1-10) ...
-Setting up libmagic1:mipsel (1:5.11-2.1) ...
-Setting up libpcre3:mipsel (1:8.31-2) ...
-Setting up libxml2:mipsel (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:mipsel (3.0.10-3) ...
-Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-5) ...
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_mipsel.deb ...
+Unpacking zlib1g-dev:mipsel (1:1.2.8.dfsg-2) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up libpipeline1:mipsel (1.3.1-1) ...
+Setting up groff-base (1.22.2-8) ...
+Setting up man-db (2.7.0.1-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up bash-completion (1:2.1-4) ...
+Setting up libasprintf0c2:mipsel (0.19.2-2) ...
+Setting up libmagic1:mipsel (1:5.19-2) ...
+Setting up libxml2:mipsel (2.9.1+dfsg1-4) ...
+Setting up libffi6:mipsel (3.1-2) ...
+Setting up libglib2.0-0:mipsel (2.42.0-1) ...
No schema files found: doing nothing.
-Setting up libcroco3:mipsel (0.6.6-2) ...
-Setting up libunistring0:mipsel (0.9.3-5) ...
-Setting up libgettextpo0:mipsel (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:mipsel (0.18.1.1-10) ...
-Setting up libgettextpo-dev:mipsel (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
+Setting up libcroco3:mipsel (0.6.8-3) ...
+Setting up libhts1:mipsel (1.1-1) ...
+Setting up libunistring0:mipsel (0.9.3-5.2) ...
+Setting up file (1:5.19-2) ...
+Setting up gettext-base (0.19.2-2) ...
+Setting up gettext (0.19.2-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:mipsel (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:mipsel (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1. [...]
+Setting up po-debconf (1.0.16+nmu3) ...
+Setting up debhelper (9.20140817) ...
+Setting up libhts-dev:mipsel (1.1-1) ...
+Setting up libtinfo-dev:mipsel (5.9+20140913-1) ...
+Setting up libncurses5-dev:mipsel (5.9+20140913-1) ...
+Setting up tabix (1.1-1) ...
+Setting up zlib1g-dev:mipsel (1:1.2.8.dfsg-2) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-11) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 3.14-0.bpo.2-loongson-2e mipsel (mips64)
+Toolchain package versions: binutils_2.24.51.20140918-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-15 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 linux-libc-dev_3.16.3-2
+Package versions: apt_1.0.9.1 base-files_7.5 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140918-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-15 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,642 +300,1615 @@ Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.1
+dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying dynamic-build.patch
+dpkg-source: info: applying debian-changes
Check disc space
────────────────
+Sufficient free space for build
+
+User Environment
+────────────────
+
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=sid-mipsel-sbuild
+SCHROOT_CHROOT_NAME=sid-mipsel-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-mipsel-sbuild-9da2abb3-05c8-4f5b-adf5-e24ce4b9aa67
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
+dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.1
dpkg-buildpackage: host architecture mipsel
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j1 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f TAGS
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_auto_configure -a -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j1 HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a "CFLAGS=-g -O2 -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.1"' > version.h
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_mipsel.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.19-1_mipsel.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0924
-
-samtools_0.1.19-1_mipsel.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: mipsel
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 403caf7143bf1b0b949196cf55cbd1d1768f15d5 555674 samtools_0.1.19-1_mipsel.deb
- 271275f5ed7142222ac09a9549835fb3c72c542b 131464 libbam-dev_0.1.19-1_mipsel.deb
-Checksums-Sha256:
- 07ca0979fd1bb36fa4702e2f481309bf72b72e6634a306e5d3a8e9570509f099 555674 samtools_0.1.19-1_mipsel.deb
- 68096b1306f84e6e4014eaa37e6cb444cf51fc927245a65f88d793407cb82301 131464 libbam-dev_0.1.19-1_mipsel.deb
-Files:
- 44d1f7279db85e98bfe8666397f898ef 555674 science optional samtools_0.1.19-1_mipsel.deb
- 6d14454cb9202d9a7fcf084e040f43a8 131464 libdevel optional libbam-dev_0.1.19-1_mipsel.deb
+padding.c:199:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
+ fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+ ^
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lcurse [...]
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+misc/ace2sam.c: In function 'main':
+misc/ace2sam.c:112:13: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=]
+ fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
+ ^
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+test/merge/test_rtrans_build.c: In function 'main':
+test/merge/test_rtrans_build.c:79:29: warning: overflow in implicit constant conversion [-Woverflow]
+ const long GIMIC_SEED = 0x1234abcd330e;
+ ^
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+test/merge/test_trans_tbl_init.c: In function 'main':
+test/merge/test_trans_tbl_init.c:323:31: warning: overflow in implicit constant conversion [-Woverflow]
+ const long GIMMICK_SEED = 0x1234abcd330e;
+ ^
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j1 test HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+make[2]: Entering directory '/«PKGBUILDDIR»'
+REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/ThgE2wBlHt/bgzip.dat.gz
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/ThgE2wBlHt/bgzip.dat.gz
+.. ok
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/ThgE2wBlHt/bgzip.dat.gz
+.. ok
-samtools_0.1.19-1_mipsel.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 555674 bytes: control archive= 1937 bytes.
- 32 bytes, 1 lines conffiles
- 793 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1439
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: processing sequence alignments in SAM and BAM formats
- Samtools is a set of utilities that manipulate nucleotide sequence alignments
- in the binary BAM format. It imports from and exports to the ascii SAM
- (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- to retrieve reads in any regions swiftly. It is designed to work on a stream,
- and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 09:23 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2013-03-30 09:23 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 09:23 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 09:23 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:24 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/bin/
--rwxr-xr-x root/root 176252 2013-03-30 09:24 ./usr/bin/bcftools
--rwxr-xr-x root/root 31780 2013-03-30 09:24 ./usr/bin/razip
--rwxr-xr-x root/root 483460 2013-03-30 09:24 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/lib/samtools/
--rwxr-xr-x root/root 18508 2013-03-30 09:24 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 18192 2013-03-30 09:24 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 207416 2013-03-30 09:24 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 10032 2013-03-30 09:24 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10032 2013-03-30 09:24 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 14224 2013-03-30 09:24 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 10068 2013-03-30 09:24 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 09:23 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_mipsel.deb
-──────────────────────────────
+/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
- new debian package, version 2.0.
- size 131464 bytes: control archive= 924 bytes.
- 713 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 441
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/lib/
--rw-r--r-- root/root 328990 2013-03-30 09:24 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/include/samtools/
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
+/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
+/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
+/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ca64eee5-03d6-4a10-836c-decf0e5e9b54/build/buildd-samtools_0.1.19-1-mipsel-muFrrg
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- bash-completion* bsdmainutils* cdbs* debhelper* diffstat* file* gettext*
- gettext-base* groff-base* html2text* intltool-debian* libasprintf-dev*
- libasprintf0c2* libcroco3* libffi5* libgettextpo-dev* libgettextpo0*
- libglib2.0-0* libmagic1* libncurses5-dev* libpcre3* libpipeline1*
- libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 29 to remove and 2 not upgraded.
-After this operation, 30.2 MB disk space will be freed.
-(Reading database ... 13074 files and directories currently installed.)
-Removing bash-completion ...
-Purging configuration files for bash-completion ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing cdbs ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libasprintf-dev:mipsel ...
-Removing libasprintf0c2:mipsel ...
-Removing libcroco3:mipsel ...
-Purging configuration files for libcroco3:mipsel ...
-Removing libglib2.0-0:mipsel ...
-Purging configuration files for libglib2.0-0:mipsel ...
-Removing libffi5:mipsel ...
-Purging configuration files for libffi5:mipsel ...
-Removing libgettextpo-dev:mipsel ...
-Removing libgettextpo0:mipsel ...
-Removing libmagic1:mipsel ...
-Purging configuration files for libmagic1:mipsel ...
-Removing libncurses5-dev ...
-Removing libpcre3:mipsel ...
-Purging configuration files for libpcre3:mipsel ...
-Removing libpipeline1:mipsel ...
-Purging configuration files for libpipeline1:mipsel ...
-Removing libtinfo-dev:mipsel ...
-Removing libunistring0:mipsel ...
-Purging configuration files for libunistring0:mipsel ...
-Removing libxml2:mipsel ...
-Purging configuration files for libxml2:mipsel ...
-Removing zlib1g-dev:mipsel ...
+/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
+/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
-Architecture: mipsel
-Build-Space: 12852
-Build-Time: 342
-Distribution: sid
-Install-Time: 58
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 479
-Source-Version: 0.1.19-1
-Space: 12852
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0924
-Build needed 00:07:59, 12852k disc space
-Signature with key '4A2D13C7' requested:
+test_index:
+ /«PKGBUILDDIR»/samtools index /tmp/ThgE2wBlHt/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/ThgE2wBlHt/large_chrom.bam ref2
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/dat/large_chrom.out
+ /«PKGBUILDDIR»/test/dat/large_chrom.out.new
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/ThgE2wBlHt/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/ThgE2wBlHt/mpileup.bam.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/ThgE2wBlHt/mpileup.cram.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/ThgE2wBlHt/mpileup.bam.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/ThgE2wBlHt/mpileup.cram.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/ThgE2wBlHt/mpileup.cram.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/ThgE2wBlHt/mpileup.cram.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ThgE2wBlHt/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ThgE2wBlHt/mpileup.1.cram | grep -v mpileup
+test/test.pl: module IO::Pty not found; skipping usage tests
+.. ok
+
+test_usage:
+ samtools
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM
+ SAM files differ at /tmp/ThgE2wBlHt/view.test001.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test001.bam -b /tmp/ThgE2wBlHt/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test001.bam.sam /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 2: SAM -> uncompressed BAM .. ok
+
+ 3: uncompressed BAM -> SAM and compare
+ SAM files differ at /tmp/ThgE2wBlHt/view.test003.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test003.sam -h /tmp/ThgE2wBlHt/view.test002.bam
+
+
+.. failed ...
+
+ 4: SAM -> fast compressed BAM .. ok
+
+ 5: fast compressed BAM -> SAM and compare
+ SAM files differ at /tmp/ThgE2wBlHt/view.test005.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test005.sam -h /tmp/ThgE2wBlHt/view.test004.bam
+
+
+.. failed ...
+
+ 6: SAM -> CRAM -> SAM (UR header tags)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test006.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test006.cram -C /tmp/ThgE2wBlHt/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test006.cram.sam /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 7: SAM -> CRAM -> SAM (M5 header tags)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test007.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test007.cram -C /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test007.cram.sam /tmp/ThgE2wBlHt/view.test007.cram
+
+
+.. failed ...
+
+ 8: BAM -> CRAM with UR -> SAM
+ SAM files differ at /tmp/ThgE2wBlHt/view.test008.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test008.cram -C /tmp/ThgE2wBlHt/view.test001.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test008.cram.sam /tmp/ThgE2wBlHt/view.test008.cram
+
+
+.. failed ...
+
+ 9: SAM -> BAM (M5 header tags)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test009.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test009.bam -b /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test009.bam.sam /tmp/ThgE2wBlHt/view.test009.bam
+
+
+.. failed ...
+
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test010.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test010.cram -C /tmp/ThgE2wBlHt/view.test009.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test010.cram.sam /tmp/ThgE2wBlHt/view.test010.cram
+
+
+.. failed ...
+
+ 11: CRAM -> BAM with UR
+ SAM files differ at /tmp/ThgE2wBlHt/view.test011.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test011.bam -b /tmp/ThgE2wBlHt/view.test008.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test011.bam.sam /tmp/ThgE2wBlHt/view.test011.bam
+
+
+.. failed ...
+
+ 12: CRAM -> BAM with M5
+ SAM files differ at /tmp/ThgE2wBlHt/view.test012.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test012.bam -b /tmp/ThgE2wBlHt/view.test010.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test012.bam.sam /tmp/ThgE2wBlHt/view.test012.bam
+
+
+.. failed ...
+
+ 13: SAM -> SAM via stdout
+ SAM files differ at /tmp/ThgE2wBlHt/view.test013.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -h /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 14: SAM -> BAM via stdout .. ok
+
+ 15: SAM -> CRAM via stdout
+ SAM files differ at /tmp/ThgE2wBlHt/view.test015.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -C /tmp/ThgE2wBlHt/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test015.cram.sam /tmp/ThgE2wBlHt/view.test015.cram
+
+
+.. failed ...
+
+ 16: SAM from stdin -> SAM
+ SAM files differ at /tmp/ThgE2wBlHt/view.test016.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test016.sam -h -
+
+
+.. failed ...
+
+ 17: BAM from stdin -> SAM
+ SAM files differ at /tmp/ThgE2wBlHt/view.test017.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test017.sam -h -
+
+
+.. failed ...
+
+ 18: CRAM from stdin -> SAM
+ SAM files differ at /tmp/ThgE2wBlHt/view.test018.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test018.sam -h -
+
+
+.. failed ...
+
+ 19: samtools view -H (SAM input) .. ok
+
+ 20: samtools view -H (BAM input) .. ok
+
+ 21: samtools view -H (CRAM input) .. ok
+
+ 22: No headers (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test022.body : 6 / /tmp/ThgE2wBlHt/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test022.body /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 23: No headers (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test023.body : 6 / /tmp/ThgE2wBlHt/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test023.body /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 24: No headers (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test024.body : 6 / /tmp/ThgE2wBlHt/view.001.body.sam : 6
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test024.body /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 25: Filter -f 128 (SAM input) .. ok
+
+ 26: Count -f 128 (SAM input) .. ok
+
+ 27: Filter -f 128 (BAM input) .. ok
+
+ 28: Count -f 128 (BAM input) .. ok
+
+ 29: Filter -f 128 (CRAM input) .. ok
+
+ 30: Count -f 128 (CRAM input) .. ok
+
+ 31: Filter -F 128 (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test031.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test031.sam -h -F 128 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 32: Count -F 128 (SAM input) .. ok
+
+ 33: Filter -F 128 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test033.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test033.sam -h -F 128 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 34: Count -F 128 (BAM input) .. ok
+
+ 35: Filter -F 128 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test035.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test035.sam -h -F 128 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 36: Count -F 128 (CRAM input) .. ok
+
+ 37: Filter -F 128 -f 2 (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test037.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test037.sam -h -F 128 -f 2 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 38: Count -F 128 -f 2 (SAM input) .. ok
+
+ 39: Filter -F 128 -f 2 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test039.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test039.sam -h -F 128 -f 2 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 40: Count -F 128 -f 2 (BAM input) .. ok
+
+ 41: Filter -F 128 -f 2 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test041.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128req2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test041.sam -h -F 128 -f 2 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 42: Count -F 128 -f 2 (CRAM input) .. ok
+
+ 43: Filter -r grp2 (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test043.sam : 29 / /tmp/ThgE2wBlHt/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test043.sam -h -r grp2 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 44: Count -r grp2 (SAM input) .. ok
+
+ 45: Filter -r grp2 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test045.sam : 29 / /tmp/ThgE2wBlHt/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test045.sam -h -r grp2 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 46: Count -r grp2 (BAM input) .. ok
+
+ 47: Filter -r grp2 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test047.sam : 29 / /tmp/ThgE2wBlHt/view.001.rg_grp2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test047.sam -h -r grp2 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 48: Count -r grp2 (CRAM input) .. ok
+
+ 49: Filter -R /tmp/ThgE2wBlHt/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/ThgE2wBlHt/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/ThgE2wBlHt/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/ThgE2wBlHt/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/ThgE2wBlHt/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/ThgE2wBlHt/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test055.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test055.sam -h -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 56: Count -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test057.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test057.sam -h -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 58: Count -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test059.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test059.sam -h -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 60: Count -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test061.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test061.sam -h -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 62: Count -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test063.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test063.sam -h -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 64: Count -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test065.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test065.sam -h -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 66: Count -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (CRAM input).. ok
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 67: Filter -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test067.sam -h -l Library 2 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 68: Count -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 69: Filter -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test069.sam -h -l Library 2 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 70: Count -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 71: Filter -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test071.sam -h -l Library 2 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 72: Count -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. expected failure
+
+ 73: Filter -q 50 (SAM input) .. ok
+
+ 74: Count -q 50 (SAM input) .. ok
+
+ 75: Filter -q 50 (BAM input) .. ok
+
+ 76: Count -q 50 (BAM input) .. ok
+
+ 77: Filter -q 50 (CRAM input) .. ok
+
+ 78: Count -q 50 (CRAM input) .. ok
+
+ 79: Filter -q 99 (SAM input) .. ok
+
+ 80: Count -q 99 (SAM input) .. ok
+
+ 81: Filter -q 99 (BAM input) .. ok
+
+ 82: Count -q 99 (BAM input) .. ok
+
+ 83: Filter -q 99 (CRAM input) .. ok
+
+ 84: Count -q 99 (CRAM input) .. ok
+
+ 85: Filter -q 100 (SAM input) .. ok
+
+ 86: Count -q 100 (SAM input) .. ok
+
+ 87: Filter -q 100 (BAM input) .. ok
+
+ 88: Count -q 100 (BAM input) .. ok
+
+ 89: Filter -q 100 (CRAM input) .. ok
+
+ 90: Count -q 100 (CRAM input) .. ok
+
+ 91: Filter -x fa (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test091.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test091.sam -h -x fa /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 92: Count -x fa (SAM input) .. ok
+
+ 93: Filter -x fa (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test093.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test093.sam -h -x fa /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 94: Count -x fa (BAM input) .. ok
+
+ 95: Filter -x fa (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test095.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test095.sam -h -x fa /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 96: Count -x fa (CRAM input) .. ok
+
+ 97: Filter -x fa -x ha (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test097.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test097.sam -h -x fa -x ha /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 98: Count -x fa -x ha (SAM input) .. ok
+
+ 99: Filter -x fa -x ha (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test099.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test099.sam -h -x fa -x ha /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 100: Count -x fa -x ha (BAM input) .. ok
+
+ 101: Filter -x fa -x ha (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test101.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test101.sam -h -x fa -x ha /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 102: Count -x fa -x ha (CRAM input) .. ok
+
+ 103: Filter -x fa -r grp2 (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test103.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test103.sam -h -x fa -r grp2 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 104: Count -x fa -r grp2 (SAM input) .. ok
+
+ 105: Filter -x fa -r grp2 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test105.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test105.sam -h -x fa -r grp2 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+ 106: Count -x fa -r grp2 (BAM input) .. ok
+
+ 107: Filter -x fa -r grp2 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test107.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg1.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test107.sam -h -x fa -r grp2 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 108: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 109: Filter -x RG -r grp2 (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test109.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test109.sam -h -x RG -r grp2 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 110: Count -x RG -r grp2 (SAM input) .. ok
+
+ 111: Filter -x RG -r grp2 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test111.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test111.sam -h -x RG -r grp2 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 112: Count -x RG -r grp2 (BAM input) .. ok
+
+ 113: Filter -x RG -r grp2 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test113.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg2.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test113.sam -h -x RG -r grp2 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 114: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 115: Filter -m 10 (SAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test115.sam : 34 / /tmp/ThgE2wBlHt/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test115.sam -h -m 10 /tmp/ThgE2wBlHt/view.001.sam
+
+
+.. failed ...
+
+ 116: Count -m 10 (SAM input) .. ok
+
+ 117: Filter -m 10 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test117.sam : 34 / /tmp/ThgE2wBlHt/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test117.sam -h -m 10 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 118: Count -m 10 (BAM input) .. ok
+
+ 119: Filter -m 10 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test119.sam : 34 / /tmp/ThgE2wBlHt/view.001.qlen10.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test119.sam -h -m 10 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 120: Count -m 10 (CRAM input) .. ok
+
+ 121: Filter -m 11 (SAM input) .. ok
+
+ 122: Count -m 11 (SAM input) .. ok
+
+ 123: Filter -m 11 (BAM input) .. ok
+
+ 124: Count -m 11 (BAM input) .. ok
+
+ 125: Filter -m 11 (CRAM input) .. ok
+
+ 126: Count -m 11 (CRAM input) .. ok
+
+ 127: Filter -m 15 (SAM input) .. ok
+
+ 128: Count -m 15 (SAM input) .. ok
+
+ 129: Filter -m 15 (BAM input) .. ok
+
+ 130: Count -m 15 (BAM input) .. ok
+
+ 131: Filter -m 15 (CRAM input) .. ok
+
+ 132: Count -m 15 (CRAM input) .. ok
+
+ 133: Filter -m 16 (SAM input) .. ok
+
+ 134: Count -m 16 (SAM input) .. ok
+
+ 135: Filter -m 16 (BAM input) .. ok
+
+ 136: Count -m 16 (BAM input) .. ok
+
+ 137: Filter -m 16 (CRAM input) .. ok
+
+ 138: Count -m 16 (CRAM input) .. ok
+
+ 139: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 140: Region Z (BAM input) .. ok
+
+ 141: Count Z (BAM input) .. ok
+
+ 142: Region Z (CRAM input) .. ok
+
+ 143: Count Z (CRAM input) .. ok
+
+ 144: Region Z:30 (BAM input) .. ok
+
+ 145: Count Z:30 (BAM input) .. ok
+
+ 146: Region Z:30 (CRAM input) .. ok
+
+ 147: Count Z:30 (CRAM input) .. ok
+
+ 148: Region Z:20-40 (BAM input) .. ok
+
+ 149: Count Z:20-40 (BAM input) .. ok
+
+ 150: Region Z:20-40 (CRAM input) .. ok
+
+ 151: Count Z:20-40 (CRAM input) .. ok
+
+ 152: Region ref1 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test152.sam : 34 / /tmp/ThgE2wBlHt/view.reg1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test152.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1
+
+
+.. failed ...
+
+ 153: Count ref1 (BAM input) .. ok
+
+ 154: Region ref1 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test154.sam : 34 / /tmp/ThgE2wBlHt/view.reg1.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test154.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1
+
+
+.. failed ...
+
+ 155: Count ref1 (CRAM input) .. ok
+
+ 156: Region ref1:15 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test156.sam : 31 / /tmp/ThgE2wBlHt/view.reg2.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test156.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15
+
+
+.. failed ...
+
+ 157: Count ref1:15 (BAM input) .. ok
+
+ 158: Region ref1:15 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test158.sam : 31 / /tmp/ThgE2wBlHt/view.reg2.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test158.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15
+
+
+.. failed ...
+
+ 159: Count ref1:15 (CRAM input) .. ok
+
+ 160: Region ref1:15-45 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test160.sam : 31 / /tmp/ThgE2wBlHt/view.reg3.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test160.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45
+
+
+.. failed ...
+
+ 161: Count ref1:15-45 (BAM input) .. ok
+
+ 162: Region ref1:15-45 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test162.sam : 31 / /tmp/ThgE2wBlHt/view.reg3.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test162.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45
+
+
+.. failed ...
+
+ 163: Count ref1:15-45 (CRAM input) .. ok
+
+ 164: Region ref1:15-45 ref2 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test164.sam : 31 / /tmp/ThgE2wBlHt/view.reg4.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test164.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45 ref2
+
+
+.. failed ...
+
+ 165: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 166: Region ref1:15-45 ref2 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test166.sam : 31 / /tmp/ThgE2wBlHt/view.reg4.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test166.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45 ref2
+
+
+.. failed ...
+
+ 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 168: Region ref1:15-45 ref2:16 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test168.sam : 31 / /tmp/ThgE2wBlHt/view.reg5.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test168.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45 ref2:16
+
+
+.. failed ...
+
+ 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 170: Region ref1:15-45 ref2:16 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test170.sam : 31 / /tmp/ThgE2wBlHt/view.reg5.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test170.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45 ref2:16
+
+
+.. failed ...
+
+ 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 172: Region ref1:15-45 ref2:16-31 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test172.sam : 31 / /tmp/ThgE2wBlHt/view.reg6.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test172.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45 ref2:16-31
+
+
+.. failed ...
+
+ 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test174.sam : 31 / /tmp/ThgE2wBlHt/view.reg6.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test174.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45 ref2:16-31
+
+
+.. failed ...
+
+ 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 176: Region ref1:15-15 ref1:45-45 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test176.sam : 31 / /tmp/ThgE2wBlHt/view.reg7.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test176.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-15 ref1:45-45
+
+
+.. failed ...
+
+ 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test178.sam : 31 / /tmp/ThgE2wBlHt/view.reg7.sam : 31
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test178.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-15 ref1:45-45
+
+
+.. failed ...
+
+ 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 180: Region -f 128 ref1 (BAM input) .. ok
+
+ 181: Count -f 128 ref1 (BAM input) .. ok
+
+ 182: Region -f 128 ref1 (CRAM input) .. ok
+
+ 183: Count -f 128 ref1 (CRAM input) .. ok
+
+ 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 188: Region -r grp2 ref1:15-45 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test188.sam : 28 / /tmp/ThgE2wBlHt/view.reg10.sam : 28
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test188.sam -h -r grp2 /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45
+
+
+.. failed ...
+
+ 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 190: Region -r grp2 ref1:15-45 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test190.sam : 28 / /tmp/ThgE2wBlHt/view.reg10.sam : 28
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test190.sam -h -r grp2 /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45
+
+
+.. failed ...
+
+ 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test200.sam : 33 / /tmp/ThgE2wBlHt/view.bed1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test200.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test202.sam : 33 / /tmp/ThgE2wBlHt/view.bed1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test202.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test204.sam : 34 / /tmp/ThgE2wBlHt/view.bed2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test204.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test206.sam : 34 / /tmp/ThgE2wBlHt/view.bed2.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test206.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test224.sam : 33 / /tmp/ThgE2wBlHt/view.bed1r1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test224.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/ThgE2wBlHt/view.test001.bam ref1:11-16
+
+
+.. failed ...
+
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test226.sam : 33 / /tmp/ThgE2wBlHt/view.bed1r1.sam : 33
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test226.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/ThgE2wBlHt/view.test006.cram ref1:11-16
+
+
+.. failed ...
+
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test240.sam : 29 / /tmp/ThgE2wBlHt/view.bed1f3.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test240.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/ThgE2wBlHt/view.test001.bam
+
+
+.. failed ...
+
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test242.sam : 29 / /tmp/ThgE2wBlHt/view.bed1f3.sam : 29
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test242.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/ThgE2wBlHt/view.test006.cram
+
+
+.. failed ...
+
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 248: Make BAM with no M5/UR tags
+ SAM files differ at /tmp/ThgE2wBlHt/view.001.no_sq.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.001.no_sq.bam -b /tmp/ThgE2wBlHt/view.001.no_m5.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.001.no_sq.bam.sam /tmp/ThgE2wBlHt/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 249: Add @SQ with -t (SAM -> SAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test249.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test249.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.sam
+
+
+.. failed ...
+
+ 250: Add @SQ with -T (SAM -> SAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test250.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test250.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.sam
+
+
+.. failed ...
+
+ 251: Add @SQ with -t (BAM -> SAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test251.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test251.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 252: Add @SQ with -T (BAM -> SAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test252.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test252.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.bam
+
+
+.. failed ...
+
+ 253: Add @SQ with -t (SAM -> BAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test253.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test253.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test253.bam.sam /tmp/ThgE2wBlHt/view.test253.bam
+
+
+.. failed ...
+
+ 254: Add @SQ with -T (SAM -> BAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test254.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test254.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test254.bam.sam /tmp/ThgE2wBlHt/view.test254.bam
+
+
+.. failed ...
+
+ 255: Add @SQ with -t (BAM -> BAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test255.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test255.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test255.bam.sam /tmp/ThgE2wBlHt/view.test255.bam
+
+
+.. failed ...
+
+ 256: Add @SQ with -T (BAM -> BAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test256.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test256.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test256.bam.sam /tmp/ThgE2wBlHt/view.test256.bam
+
+
+.. failed ...
+
+ 257: Add @SQ with -t (SAM -> CRAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test257.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test257.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test257.cram.sam /tmp/ThgE2wBlHt/view.test257.cram
+
+
+.. failed ...
+
+ 258: Add @SQ with -T (SAM -> CRAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test258.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test258.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test258.cram.sam /tmp/ThgE2wBlHt/view.test258.cram
+
+
+.. failed ...
+
+ 259: Add @SQ with -t (BAM -> CRAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test259.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test259.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test259.cram.sam /tmp/ThgE2wBlHt/view.test259.cram
+
+
+.. failed ...
+
+ 260: Add @SQ with -T (BAM -> CRAM)
+ SAM files differ at /tmp/ThgE2wBlHt/view.test260.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test260.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test260.cram.sam /tmp/ThgE2wBlHt/view.test260.cram
+
+
+.. failed ...
+
+ 261: CIGAR B-operator removal .. ok
+
+ 262: Big SAM -> BAM .. ok
+
+ 263: Big SAM -> BAM (2 threads) .. ok
+
+ 264: Big SAM -> BAM (4 threads) .. ok
+
+ 265: Big SAM -> CRAM .. ok
+
+ 266: Big SAM -> CRAM (2 threads) .. ok
+
+ 267: Big SAM -> CRAM (4 threads) .. ok
+
+ 268: Subsample 0.2 (SAM input) ............ ok
+
+ 269: Subsample 0.5 (SAM input) ............ ok
+
+ 270: Subsample 0.8 (SAM input) ............ ok
+
+ 271: Subsample 0.2 (BAM input) ............ ok
+
+ 272: Subsample 0.5 (BAM input) ............ ok
+
+ 273: Subsample 0.8 (BAM input) ............ ok
+
+ 274: Subsample 0.2 (CRAM input) ............ ok
+
+ 275: Subsample 0.5 (CRAM input) ............ ok
+
+ 276: Subsample 0.8 (CRAM input) ............ ok
+
+test_cat:
+ Generating test data file .................. done
+ Generate BAM file #1 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #2 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #3 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #4 .. ok
+
+ 1: cat BAM files .. ok
+
+ 2: cat recompressed BAM files .. ok
+
+ 3: cat BAM files to stdout .. ok
+
+ 4: cat recompressed BAM files to stdout .. ok
+
+ 5: cat BAM files with new header .. ok
+
+ 6: cat recompressed BAM files with new header .. ok
+
+test_bam2fq:
+ Generate BAM file
+ SAM files differ at GLOB(0xc2eca0) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/bam2fq.001.bam -b /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/ThgE2wBlHt/bam2fq.001.bam
+
+
+.. failed ...
+
+ Generate CRAM file
+ SAM files differ at GLOB(0xd42a60) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/bam2fq.001.cram -C /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/ThgE2wBlHt/bam2fq.001.cram
+
+
+.. failed ...
+
+[M::main_bam2fq] processed 36 reads
+ 1: bam2fq (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 2: bam2fq -n (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 3: bam2fq (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 4: bam2fq -n (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 5: bam2fq (CRAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 6: bam2fq -n (CRAM input) .. ok
+
+test_depad:
+ Generate BAM file .. ok
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/ThgE2wBlHt/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/ThgE2wBlHt/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/ThgE2wBlHt/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/ThgE2wBlHt/depad.001p.bam
+
+
+.. expected failure
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+/bin/bash: line 1: 8686 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/BeihiK_0lz
+
+.. expected failure
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/ZQ1oSRFZSQ - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+
+.. expected failure
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/2_isize_overflow.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/3_reverse_read_pp_lt.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/4_reverse_read_pp_equal.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/5_ct.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
+.. ok
+
+test_idxstat:
+ /«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+
+Number of tests:
+ total .. 342
+ passed .. 237
+ failed .. 87
+ expected failure .. 18
+ unexpected pass .. 0
+
+make[2]: *** [test] Error 1
+Makefile:183: recipe for target 'test' failed
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+dh_auto_test: make -j1 test HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip returned exit code 2
+make[1]: *** [override_dh_auto_test] Error 2
+debian/rules:18: recipe for target 'override_dh_auto_test' failed
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+make: *** [build-arch] Error 2
+debian/rules:6: recipe for target 'build-arch' failed
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20140925-0228
+
+Finished
+────────
+
+E: Build failure (dpkg-buildpackage died)
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build Architecture: mipsel
+Build-Space: 21944
+Build-Time: 837
+Distribution: sid
+Fail-Stage: build
+Host Architecture: mipsel
+Install-Time: 91
+Job: samtools_1.1-1
+Machine Architecture: mipsel
+Package: samtools
+Package-Time: 1109
+Source-Version: 1.1-1
+Space: 21944
+Status: attempted
+Version: 1.1-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20140925-0228
+Build needed 00:18:29, 21944k disc space
diff --git a/ppc64el.log b/ppc64el.log
new file mode 100644
index 0000000..a52ee78
--- /dev/null
+++ b/ppc64el.log
@@ -0,0 +1,546 @@
+From buildd at ppc64el2.debian.net Thu Sep 25 02:55:34 2014
+Return-path: <buildd at ppc64el2.debian.net>
+Received: from hall.aurel32.net ([2001:bc8:30d7:101::1])
+ by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at ppc64el2.debian.net>)
+ id 1XWzDS-0001tF-Li
+ for logs at buildd.debian.org; Thu, 25 Sep 2014 02:55:34 +0000
+Received: from [91.121.150.236] (helo=ppc64el2.debian.net)
+ by hall.aurel32.net with esmtps (TLS1.2:RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at ppc64el2.debian.net>)
+ id 1XWzDR-0005pK-3P; Thu, 25 Sep 2014 04:55:33 +0200
+Received: from buildd by ppc64el2.debian.net with local (Exim 4.84)
+ (envelope-from <buildd at ppc64el2.debian.net>)
+ id 1XWzDH-0001M0-Oc; Thu, 25 Sep 2014 04:55:23 +0200
+Content-Transfer-Encoding: binary
+MIME-Version: 1.0
+X-Mailer: MIME::Lite 3.030 (F2.85; T2.06; A2.13; B3.14; Q3.13)
+Date: Thu, 25 Sep 2014 04:55:23 +0200
+From: buildd on ppc64el2 <buildd at ppc64el2.debian.net>
+To: buildd-porters at ppc64el2.debian.net,builddlogs at aurel32.net
+Subject: Log for attempted build of samtools_1.1-1 on ppc64el (dist=sid)
+Message-Id: <E1XWzDH-0001M0-Oc at ppc64el2.debian.net>
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.64.0 (17 May 2013) on ppc64el2.debian.net
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 1.1-1 (ppc64el) 25 Sep 2014 02:24 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 1.1-1
+Source Version: 1.1-1
+Distribution: sid
+Machine Architecture: ppc64el
+Host Architecture: ppc64el
+Build Architecture: ppc64el
+
+I: NOTICE: Log filtering will replace 'build/samtools-tWy_2r/samtools-1.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-tWy_2r' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ppc64el-sbuild-a0d75f02-8cc1-4fe2-b92b-11ac6d034834' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://ftp.debian.org unstable InRelease [233 kB]
+Get:2 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:3 http://incoming.debian.org buildd-unstable/main Sources [358 kB]
+Get:4 http://ftp.debian.org unstable/main Sources [7548 kB]
+Get:5 http://incoming.debian.org buildd-unstable/contrib Sources [1136 B]
+Get:6 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
+Get:7 http://incoming.debian.org buildd-unstable/main ppc64el Packages [273 kB]
+Get:8 http://incoming.debian.org buildd-unstable/contrib ppc64el Packages [844 B]
+Get:9 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
+Get:10 http://ftp.debian.org unstable/non-free Sources [107 kB]
+Get:11 http://ftp.debian.org unstable/main ppc64el Packages [6538 kB]
+Get:12 http://ftp.debian.org unstable/contrib ppc64el Packages [38.3 kB]
+Get:13 http://ftp.fr.debian.org unstable InRelease [233 kB]
+Get:14 http://ftp.fr.debian.org unstable/main Sources [7548 kB]
+Get:15 http://ftp.fr.debian.org unstable/contrib Sources [57.1 kB]
+Get:16 http://ftp.fr.debian.org unstable/non-free Sources [107 kB]
+Get:17 http://ftp.fr.debian.org unstable/main ppc64el Packages [6538 kB]
+Get:18 http://ftp.fr.debian.org unstable/contrib ppc64el Packages [38.3 kB]
+Fetched 29.8 MB in 5s (5242 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 4333 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
+Fetched 4333 kB in 0s (6428 kB/s)
+Download complete and in download only mode
+
+Check arch
+──────────
+
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-CckoiP/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded.
+Need to get 0 B/820 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ... 11706 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-4i5qbP/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf sysvinit tabix zlib1g-dev
+Suggested packages:
+ wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
+ www-browser libmail-box-perl
+Recommended packages:
+ curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
+ libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ libmail-sendmail-perl
+The following NEW packages will be installed:
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
+ libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy sysvinit tabix
+ zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 10 not upgraded.
+Need to get 9950 kB/9951 kB of archives.
+After this operation, 31.9 MB of additional disk space will be used.
+Get:1 http://ftp.fr.debian.org/debian/ unstable/main libpipeline1 ppc64el 1.3.1-1 [25.0 kB]
+Get:2 http://ftp.fr.debian.org/debian/ unstable/main groff-base ppc64el 1.22.2-8 [1216 kB]
+Get:3 http://ftp.fr.debian.org/debian/ unstable/main bsdmainutils ppc64el 9.0.5+b1 [180 kB]
+Get:4 http://ftp.fr.debian.org/debian/ unstable/main man-db ppc64el 2.7.0.1-1 [980 kB]
+Get:5 http://ftp.fr.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
+Get:6 http://ftp.fr.debian.org/debian/ unstable/main libasprintf0c2 ppc64el 0.19.2-2 [30.9 kB]
+Get:7 http://ftp.fr.debian.org/debian/ unstable/main libmagic1 ppc64el 1:5.19-2+b1 [235 kB]
+Get:8 http://ftp.fr.debian.org/debian/ unstable/main libxml2 ppc64el 2.9.1+dfsg1-4+b1 [731 kB]
+Get:9 http://ftp.fr.debian.org/debian/ unstable/main libffi6 ppc64el 3.1-2+b1 [20.4 kB]
+Get:10 http://ftp.fr.debian.org/debian/ unstable/main libglib2.0-0 ppc64el 2.42.0-1 [2360 kB]
+Get:11 http://ftp.fr.debian.org/debian/ unstable/main libcroco3 ppc64el 0.6.8-3+b1 [125 kB]
+Get:12 http://ftp.fr.debian.org/debian/ unstable/main libhts1 ppc64el 1.1-1 [192 kB]
+Get:13 http://ftp.fr.debian.org/debian/ unstable/main libunistring0 ppc64el 0.9.3-5.2+b1 [263 kB]
+Get:14 http://ftp.fr.debian.org/debian/ unstable/main sysvinit ppc64el 2.88dsf-53.4 [98.5 kB]
+Get:15 http://ftp.fr.debian.org/debian/ unstable/main file ppc64el 1:5.19-2+b1 [58.5 kB]
+Get:16 http://ftp.fr.debian.org/debian/ unstable/main gettext-base ppc64el 0.19.2-2 [118 kB]
+Get:17 http://ftp.fr.debian.org/debian/ unstable/main gettext ppc64el 0.19.2-2 [1190 kB]
+Get:18 http://ftp.fr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:19 http://ftp.fr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
+Get:20 http://ftp.fr.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
+Get:21 http://ftp.fr.debian.org/debian/ unstable/main libhts-dev ppc64el 1.1-1 [246 kB]
+Get:22 http://ftp.fr.debian.org/debian/ unstable/main libtinfo-dev ppc64el 5.9+20140913-1 [77.9 kB]
+Get:23 http://ftp.fr.debian.org/debian/ unstable/main libncurses5-dev ppc64el 5.9+20140913-1 [175 kB]
+Get:24 http://ftp.fr.debian.org/debian/ unstable/main tabix ppc64el 1.1-1 [174 kB]
+Get:25 http://ftp.fr.debian.org/debian/ unstable/main zlib1g-dev ppc64el 1:1.2.8.dfsg-2+b1 [206 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 9950 kB in 3s (2767 kB/s)
+Selecting previously unselected package libpipeline1:ppc64el.
+(Reading database ... 11706 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.3.1-1_ppc64el.deb ...
+Unpacking libpipeline1:ppc64el (1.3.1-1) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.2-8_ppc64el.deb ...
+Unpacking groff-base (1.22.2-8) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.5+b1_ppc64el.deb ...
+Unpacking bsdmainutils (9.0.5+b1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.0.1-1_ppc64el.deb ...
+Unpacking man-db (2.7.0.1-1) ...
+Selecting previously unselected package bash-completion.
+Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
+Unpacking bash-completion (1:2.1-4) ...
+Selecting previously unselected package libasprintf0c2:ppc64el.
+Preparing to unpack .../libasprintf0c2_0.19.2-2_ppc64el.deb ...
+Unpacking libasprintf0c2:ppc64el (0.19.2-2) ...
+Selecting previously unselected package libmagic1:ppc64el.
+Preparing to unpack .../libmagic1_1%3a5.19-2+b1_ppc64el.deb ...
+Unpacking libmagic1:ppc64el (1:5.19-2+b1) ...
+Selecting previously unselected package libxml2:ppc64el.
+Preparing to unpack .../libxml2_2.9.1+dfsg1-4+b1_ppc64el.deb ...
+Unpacking libxml2:ppc64el (2.9.1+dfsg1-4+b1) ...
+Selecting previously unselected package libffi6:ppc64el.
+Preparing to unpack .../libffi6_3.1-2+b1_ppc64el.deb ...
+Unpacking libffi6:ppc64el (3.1-2+b1) ...
+Selecting previously unselected package libglib2.0-0:ppc64el.
+Preparing to unpack .../libglib2.0-0_2.42.0-1_ppc64el.deb ...
+Unpacking libglib2.0-0:ppc64el (2.42.0-1) ...
+Selecting previously unselected package libcroco3:ppc64el.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_ppc64el.deb ...
+Unpacking libcroco3:ppc64el (0.6.8-3+b1) ...
+Selecting previously unselected package libhts1:ppc64el.
+Preparing to unpack .../libhts1_1.1-1_ppc64el.deb ...
+Unpacking libhts1:ppc64el (1.1-1) ...
+Selecting previously unselected package libunistring0:ppc64el.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_ppc64el.deb ...
+Unpacking libunistring0:ppc64el (0.9.3-5.2+b1) ...
+Selecting previously unselected package sysvinit.
+Preparing to unpack .../sysvinit_2.88dsf-53.4_ppc64el.deb ...
+Unpacking sysvinit (2.88dsf-53.4) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.19-2+b1_ppc64el.deb ...
+Unpacking file (1:5.19-2+b1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.2-2_ppc64el.deb ...
+Unpacking gettext-base (0.19.2-2) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.2-2_ppc64el.deb ...
+Unpacking gettext (0.19.2-2) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.1) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
+Unpacking po-debconf (1.0.16+nmu3) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20140817_all.deb ...
+Unpacking debhelper (9.20140817) ...
+Selecting previously unselected package libhts-dev:ppc64el.
+Preparing to unpack .../libhts-dev_1.1-1_ppc64el.deb ...
+Unpacking libhts-dev:ppc64el (1.1-1) ...
+Selecting previously unselected package libtinfo-dev:ppc64el.
+Preparing to unpack .../libtinfo-dev_5.9+20140913-1_ppc64el.deb ...
+Unpacking libtinfo-dev:ppc64el (5.9+20140913-1) ...
+Selecting previously unselected package libncurses5-dev:ppc64el.
+Preparing to unpack .../libncurses5-dev_5.9+20140913-1_ppc64el.deb ...
+Unpacking libncurses5-dev:ppc64el (5.9+20140913-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.1-1_ppc64el.deb ...
+Unpacking tabix (1.1-1) ...
+Selecting previously unselected package zlib1g-dev:ppc64el.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_ppc64el.deb ...
+Unpacking zlib1g-dev:ppc64el (1:1.2.8.dfsg-2+b1) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up libpipeline1:ppc64el (1.3.1-1) ...
+Setting up groff-base (1.22.2-8) ...
+Setting up bsdmainutils (9.0.5+b1) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up man-db (2.7.0.1-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up bash-completion (1:2.1-4) ...
+Setting up libasprintf0c2:ppc64el (0.19.2-2) ...
+Setting up libmagic1:ppc64el (1:5.19-2+b1) ...
+Setting up libxml2:ppc64el (2.9.1+dfsg1-4+b1) ...
+Setting up libffi6:ppc64el (3.1-2+b1) ...
+Setting up libglib2.0-0:ppc64el (2.42.0-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:ppc64el (0.6.8-3+b1) ...
+Setting up libhts1:ppc64el (1.1-1) ...
+Setting up libunistring0:ppc64el (0.9.3-5.2+b1) ...
+Setting up sysvinit (2.88dsf-53.4) ...
+Setting up file (1:5.19-2+b1) ...
+Setting up gettext-base (0.19.2-2) ...
+Setting up gettext (0.19.2-2) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu3) ...
+Setting up debhelper (9.20140817) ...
+Setting up libhts-dev:ppc64el (1.1-1) ...
+Setting up libtinfo-dev:ppc64el (5.9+20140913-1) ...
+Setting up libncurses5-dev:ppc64el (5.9+20140913-1) ...
+Setting up tabix (1.1-1) ...
+Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-11) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 3.16-1-powerpc64le ppc64el (ppc64le)
+Toolchain package versions: binutils_2.24.51.20140918-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-15 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 linux-libc-dev_3.16.3-1
+Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.1 base-files_7.5+b1 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140918-1 bsdmainutils_9.0.5+b1 bsdutils_1:2.20.1-5.8+b1 build-essential_11.7+b1 bzip2_1.0.6-7+b1 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-15 dash_0.5.7-4+b1 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-2+b1 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4+b1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.90-1 dpkg_1.17.13 [...]
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.1
+dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
+dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying dynamic-build.patch
+dpkg-source: info: applying debian-changes
+
+Check disc space
+────────────────
+
+Sufficient free space for build
+
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=parallel=8
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=sid-ppc64el-sbuild
+SCHROOT_CHROOT_NAME=sid-ppc64el-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1002
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-ppc64el-sbuild-a0d75f02-8cc1-4fe2-b92b-11ac6d034834
+SCHROOT_UID=1002
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.1
+dpkg-buildpackage: host architecture ppc64el
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+ fakeroot debian/rules clean
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j8 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f TAGS
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_auto_configure -a -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j8 HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -l [...]
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j8 test HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+make[2]: Entering directory '/«PKGBUILDDIR»'
+REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/OsbUKpLXsb/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/OsbUKpLXsb/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/OsbUKpLXsb/bgzip.dat.gz
+.. ok
+
+Signal caught, cleaning and exiting...
+make[1]: *** [override_dh_auto_test] Terminated
+E: Caught signal ‘Terminated’: terminating immediately
+make[2]: *** [test] Terminated
+make: *** [build-arch] Terminated
+The command failed [15]: /«PKGBUILDDIR»/samtools faidx /tmp/OsbUKpLXsb/faidx.fa
+out:
+err:
+ at test/test.pl line 67.
+ main::error("The command failed [15]: /«PKGBUILDDIR»/"..., "out:\x{a}", "err:\x{a}") called at test/test.pl line 138
+ main::cmd("/«PKGBUILDDIR»/samtools faidx /tmp/OsbUK"...) called at test/test.pl line 390
+ main::test_faidx(HASH(0x10030693058)) called at test/test.pl line 36
+debian/rules:18: recipe for target 'override_dh_auto_test' failed
+Makefile:183: recipe for target 'test' failed
+debian/rules:6: recipe for target 'build-arch' failed
+Build killed with signal TERM after 150 minutes of inactivity
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20140925-0455
+
+Finished
+────────
+
+E: Build failure (dpkg-buildpackage died)
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build Architecture: ppc64el
+Build-Space: 44608
+Build-Time: 9005
+Distribution: sid
+Fail-Stage: build
+Host Architecture: ppc64el
+Install-Time: 9
+Job: samtools_1.1-1
+Machine Architecture: ppc64el
+Package: samtools
+Package-Time: 9026
+Source-Version: 1.1-1
+Space: 44608
+Status: attempted
+Version: 1.1-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20140925-0455
+Build needed 02:30:26, 44608k disc space
diff --git a/upload b/upload
index 4a9e718..9ff390e 100644
--- a/upload
+++ b/upload
@@ -1,7 +1,7 @@
-u samtools_0.1.19-1.dsc ftp.upload.debian.org Sat Mar 30 17:51:46 2013
-u libbam-dev_0.1.19-1_amd64.deb ftp.upload.debian.org Sat Mar 30 17:51:49 2013
-u samtools_0.1.19-1.debian.tar.gz ftp.upload.debian.org Sat Mar 30 17:51:51 2013
-u samtools_0.1.19.orig.tar.gz ftp.upload.debian.org Sat Mar 30 17:51:57 2013
-u samtools_0.1.19-1_amd64.deb ftp.upload.debian.org Sat Mar 30 17:52:02 2013
-u samtools_0.1.19-1_amd64.changes ftp.upload.debian.org Sat Mar 30 17:52:03 2013
-s samtools_0.1.19-1_amd64.changes ftp.upload.debian.org Sat Mar 30 17:52:03 2013
+u samtools_1.1-1_amd64.deb ftp.upload.debian.org Thu Sep 25 09:09:48 2014
+u samtools_1.1-1.debian.tar.xz ftp.upload.debian.org Thu Sep 25 09:09:49 2014
+u samtools-test_1.1-1_all.deb ftp.upload.debian.org Thu Sep 25 09:09:52 2014
+u samtools_1.1-1.dsc ftp.upload.debian.org Thu Sep 25 09:09:54 2014
+u samtools_1.1.orig.tar.gz ftp.upload.debian.org Thu Sep 25 09:09:57 2014
+u samtools_1.1-1_amd64.changes ftp.upload.debian.org Thu Sep 25 09:09:58 2014
+s samtools_1.1-1_amd64.changes ftp.upload.debian.org Thu Sep 25 09:09:58 2014
--
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