[med-svn] samtools 01/01: Build logs for samtools 1.1-1
Charles Plessy
plessy at moszumanska.debian.org
Thu Sep 25 12:42:37 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 0846f66256dc32b453d7342a28531b33d4b0d6af
Author: Charles Plessy <plessy at debian.org>
Date: Thu Sep 25 21:42:22 2014 +0900
Build logs for samtools 1.1-1
---
amd64.log | 2639 +++++++++++++++++++++++++++++++++++++++++++++----------------
1 file changed, 1970 insertions(+), 669 deletions(-)
diff --git a/amd64.log b/amd64.log
index 72f115a..3a44ba0 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,30 +1,30 @@
-sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on aqwa.igloo
+sbuild (Debian sbuild) 0.64.1 (13 Oct 2013) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (amd64) 30 mars 2013 17:33 ║
+║ samtools 1.1-1 (amd64) 25 sept. 2014 09:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
+Version: 1.1-1
+Source Version: 1.1-1
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/samtools-oC2Dff/samtools-0.1.19' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-oC2Dff' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-b13f39f8-12b1-4b0f-aa4e-3621693a5063' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-No0uS_/samtools-1.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-No0uS_' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-3e8fcdc5-336b-4691-bf43-e99b6e156ad7' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Hit ftp://ftp.jp.debian.org sid Release.gpg
-Hit ftp://ftp.jp.debian.org sid Release
-Hit ftp://ftp.jp.debian.org sid/main Sources/DiffIndex
-Hit ftp://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
-Hit ftp://ftp.jp.debian.org sid/main Translation-en/DiffIndex
+Hit http://ftp.jp.debian.org unstable InRelease
+Get:1 http://ftp.jp.debian.org unstable/main Sources/DiffIndex [7876 B]
+Get:2 http://ftp.jp.debian.org unstable/main amd64 Packages/DiffIndex [7876 B]
+Get:3 http://ftp.jp.debian.org unstable/main Translation-en/DiffIndex [7876 B]
+Fetched 23.6 kB in 1s (12.1 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -39,14 +39,14 @@ Reading state information...
Local sources
─────────────
-samtools_0.1.19-1.dsc exists in .; copying to chroot
+samtools_1.1-1.dsc exists in .; copying to chroot
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-5mJlIc/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-5QNb6M/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -62,15 +62,16 @@ 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 0 not upgraded.
-Need to get 0 B/714 B of archives.
+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 ... 10954 files and directories currently installed.)
-Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
+(Reading database ... 11169 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 (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-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 (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-cjyhAe/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+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-aSqs1T/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Reading package lists...
@@ -83,157 +84,141 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra 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
+ 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 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 sbuild-build-depends-samtools-dummy
+ 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, 30 newly installed, 0 to remove and 0 not upgraded.
-Need to get 9553 kB/10.4 MB of archives.
-After this operation, 29.8 MB of additional disk space will be used.
-Get:1 ftp://ftp.jp.debian.org/debian/ sid/main libpipeline1 amd64 1.2.2-2 [40.0 kB]
-Get:2 ftp://ftp.jp.debian.org/debian/ sid/main groff-base amd64 1.22.2-1 [743 kB]
-Get:3 ftp://ftp.jp.debian.org/debian/ sid/main bsdmainutils amd64 9.0.4 [210 kB]
-Get:4 ftp://ftp.jp.debian.org/debian/ sid/main man-db amd64 2.6.3-3 [898 kB]
-Get:5 ftp://ftp.jp.debian.org/debian/ sid/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 ftp://ftp.jp.debian.org/debian/ sid/main libasprintf0c2 amd64 0.18.1.1-10 [27.2 kB]
-Get:7 ftp://ftp.jp.debian.org/debian/ sid/main libmagic1 amd64 1:5.11-2.1 [202 kB]
-Get:8 ftp://ftp.jp.debian.org/debian/ sid/main libpcre3 amd64 1:8.31-2 [247 kB]
-Get:9 ftp://ftp.jp.debian.org/debian/ sid/main libxml2 amd64 2.8.0+dfsg1-7+nmu1 [904 kB]
-Get:10 ftp://ftp.jp.debian.org/debian/ sid/main libglib2.0-0 amd64 2.33.12+really2.32.4-5 [1838 kB]
-Get:11 ftp://ftp.jp.debian.org/debian/ sid/main libcroco3 amd64 0.6.6-2 [134 kB]
-Get:12 ftp://ftp.jp.debian.org/debian/ sid/main libgettextpo0 amd64 0.18.1.1-10 [145 kB]
-Get:13 ftp://ftp.jp.debian.org/debian/ sid/main file amd64 1:5.11-2.1 [51.9 kB]
-Get:14 ftp://ftp.jp.debian.org/debian/ sid/main gettext-base amd64 0.18.1.1-10 [154 kB]
-Get:15 ftp://ftp.jp.debian.org/debian/ sid/main cdbs all 0.4.120 [80.4 kB]
-Get:16 ftp://ftp.jp.debian.org/debian/ sid/main libasprintf-dev amd64 0.18.1.1-10 [26.8 kB]
-Get:17 ftp://ftp.jp.debian.org/debian/ sid/main libgettextpo-dev amd64 0.18.1.1-10 [184 kB]
-Get:18 ftp://ftp.jp.debian.org/debian/ sid/main gettext amd64 0.18.1.1-10 [1815 kB]
-Get:19 ftp://ftp.jp.debian.org/debian/ sid/main debhelper all 9.20120909 [705 kB]
-Get:20 ftp://ftp.jp.debian.org/debian/ sid/main diffstat amd64 1.55-3 [30.0 kB]
-Get:21 ftp://ftp.jp.debian.org/debian/ sid/main libtinfo-dev amd64 5.9-10 [105 kB]
-Get:22 ftp://ftp.jp.debian.org/debian/ sid/main libncurses5-dev amd64 5.9-10 [223 kB]
-Get:23 ftp://ftp.jp.debian.org/debian/ sid/main quilt all 0.60-8 [381 kB]
-Get:24 ftp://ftp.jp.debian.org/debian/ sid/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9553 kB in 24s (385 kB/s)
+0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/10.2 MB of archives.
+After this operation, 31.7 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1:amd64.
-(Reading database ... 10954 files and directories currently installed.)
-Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-2_amd64.deb) ...
+(Reading database ... 11169 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.3.1-1_amd64.deb ...
+Unpacking libpipeline1:amd64 (1.3.1-1) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_amd64.deb) ...
+Preparing to unpack .../groff-base_1.22.2-8_amd64.deb ...
+Unpacking groff-base (1.22.2-8) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_amd64.deb) ...
+Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ...
+Unpacking bsdmainutils (9.0.5) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_amd64.deb) ...
+Preparing to unpack .../man-db_2.7.0.1-1_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:amd64.
-Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10_amd64.deb) ...
+Preparing to unpack .../libasprintf0c2_0.19.2-2_amd64.deb ...
+Unpacking libasprintf0c2:amd64 (0.19.2-2) ...
Selecting previously unselected package libmagic1:amd64.
-Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.11-2.1_amd64.deb) ...
-Selecting previously unselected package libpcre3:amd64.
-Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.31-2_amd64.deb) ...
+Preparing to unpack .../libmagic1_1%3a5.19-2_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.19-2) ...
Selecting previously unselected package libxml2:amd64.
-Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-7+nmu1_amd64.deb) ...
-Selecting previously unselected package libffi5:amd64.
-Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ...
+Preparing to unpack .../libxml2_2.9.1+dfsg1-4_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.1+dfsg1-4) ...
+Selecting previously unselected package libffi6:amd64.
+Preparing to unpack .../libffi6_3.1-2_amd64.deb ...
+Unpacking libffi6:amd64 (3.1-2) ...
Selecting previously unselected package libglib2.0-0:amd64.
-Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-5_amd64.deb) ...
+Preparing to unpack .../libglib2.0-0_2.42.0-1_amd64.deb ...
+Unpacking libglib2.0-0:amd64 (2.42.0-1) ...
Selecting previously unselected package libcroco3:amd64.
-Unpacking libcroco3:amd64 (from .../libcroco3_0.6.6-2_amd64.deb) ...
+Preparing to unpack .../libcroco3_0.6.8-3_amd64.deb ...
+Unpacking libcroco3:amd64 (0.6.8-3) ...
+Selecting previously unselected package libhts1:amd64.
+Preparing to unpack .../libhts1_1.1-1_amd64.deb ...
+Unpacking libhts1:amd64 (1.1-1) ...
Selecting previously unselected package libunistring0:amd64.
-Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ...
-Selecting previously unselected package libgettextpo0:amd64.
-Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-10_amd64.deb) ...
+Preparing to unpack .../libunistring0_0.9.3-5.2_amd64.deb ...
+Unpacking libunistring0:amd64 (0.9.3-5.2) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_amd64.deb) ...
+Preparing to unpack .../file_1%3a5.19-2_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_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_amd64.deb) ...
-Selecting previously unselected package libasprintf-dev:amd64.
-Unpacking libasprintf-dev:amd64 (from .../libasprintf-dev_0.18.1.1-10_amd64.deb) ...
-Selecting previously unselected package libgettextpo-dev:amd64.
-Unpacking libgettextpo-dev:amd64 (from .../libgettextpo-dev_0.18.1.1-10_amd64.deb) ...
+Preparing to unpack .../gettext-base_0.19.2-2_amd64.deb ...
+Unpacking gettext-base (0.19.2-2) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_amd64.deb) ...
+Preparing to unpack .../gettext_0.19.2-2_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_amd64.deb) ...
+Preparing to unpack .../debhelper_9.20140817_all.deb ...
+Unpacking debhelper (9.20140817) ...
+Selecting previously unselected package libhts-dev:amd64.
+Preparing to unpack .../libhts-dev_1.1-1_amd64.deb ...
+Unpacking libhts-dev:amd64 (1.1-1) ...
Selecting previously unselected package libtinfo-dev:amd64.
-Unpacking libtinfo-dev:amd64 (from .../libtinfo-dev_5.9-10_amd64.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_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_amd64.deb ...
+Unpacking libtinfo-dev:amd64 (5.9+20140913-1) ...
+Selecting previously unselected package libncurses5-dev:amd64.
+Preparing to unpack .../libncurses5-dev_5.9+20140913-1_amd64.deb ...
+Unpacking libncurses5-dev:amd64 (5.9+20140913-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../archives/tabix_1.1-1_amd64.deb ...
+Unpacking tabix (1.1-1) ...
Selecting previously unselected package zlib1g-dev:amd64.
-Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_amd64.deb) ...
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
-Setting up libpipeline1:amd64 (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up libpipeline1: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:amd64 (0.18.1.1-10) ...
-Setting up libmagic1:amd64 (1:5.11-2.1) ...
-Setting up libpcre3:amd64 (1:8.31-2) ...
-Setting up libxml2:amd64 (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:amd64 (3.0.10-3) ...
-Setting up libglib2.0-0: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:amd64 (0.19.2-2) ...
+Setting up libmagic1:amd64 (1:5.19-2) ...
+Setting up libxml2:amd64 (2.9.1+dfsg1-4) ...
+Setting up libffi6:amd64 (3.1-2) ...
+Setting up libglib2.0-0:amd64 (2.42.0-1) ...
No schema files found: doing nothing.
-Setting up libcroco3:amd64 (0.6.6-2) ...
-Setting up libunistring0:amd64 (0.9.3-5) ...
-Setting up libgettextpo0: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:amd64 (0.18.1.1-10) ...
-Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
+Setting up libcroco3:amd64 (0.6.8-3) ...
+Setting up libhts1:amd64 (1.1-1) ...
+Setting up libunistring0: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:amd64 (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ...
+Setting up po-debconf (1.0.16+nmu3) ...
+Setting up debhelper (9.20140817) ...
+Setting up libhts-dev:amd64 (1.1-1) ...
+Setting up libtinfo-dev:amd64 (5.9+20140913-1) ...
+Setting up libncurses5-dev:amd64 (5.9+20140913-1) ...
+Setting up tabix (1.1-1) ...
+Setting up zlib1g-dev:amd64 (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_2.22-8 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_3.2.41-2
-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_4:4.7.2-1 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_1.42. [...]
+Kernel: Linux 3.16-1-amd64 amd64 (x86_64)
+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_4.3-9.1 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 debconf-i18n_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 eatmydata_26-2 fakero [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -243,13 +228,14 @@ Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (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: extracting unsigned source package (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
────────────────
@@ -262,374 +248,1195 @@ User Environment
HOME=/sbuild-nonexistent
LOGNAME=charles
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-SCHROOT_ALIAS_NAME=unstable
-SCHROOT_CHROOT_NAME=sid-amd64-sbuild
+SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
+SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-b13f39f8-12b1-4b0f-aa4e-3621693a5063
+SCHROOT_SESSION_ID=unstable-amd64-sbuild-3e8fcdc5-336b-4691-bf43-e99b6e156ad7
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
TERM=xterm
USER=charles
USERNAME=charles
-XDG_RUNTIME_DIR=/run/user/charles
+XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
-XDG_SESSION_ID=2
+XDG_SESSION_ID=115
XDG_VTNR=7
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
+dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-0.1.19
+ dpkg-source --before-build samtools-1.1
dpkg-buildpackage: host architecture 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 `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/misc'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/«PKGBUILDDIR»/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
- dpkg-source -b samtools-0.1.19
+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
+ dpkg-source -b samtools-1.1
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
dpkg-source: info: using source format `3.0 (quilt)'
-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
-dpkg-source: info: building samtools using existing ./samtools_0.1.19.orig.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.19-1.dsc
+dpkg-source: info: building samtools using existing ./samtools_1.1.orig.tar.gz
+dpkg-source: info: local changes detected, the modified files are:
+ samtools-1.1/.travis.yml
+ samtools-1.1/README.md
+ samtools-1.1/bam.h
+ samtools-1.1/test/test.pl
+dpkg-source: info: local changes have been recorded in a new patch: samtools-1.1/debian/patches/debian-changes
+dpkg-source: info: building samtools in samtools_1.1-1.debian.tar.xz
+dpkg-source: info: building samtools in samtools_1.1-1.dsc
debian/rules build
-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 `/«PKGBUILDDIR»'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-File series fully applied, ends at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-/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 `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»'
-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 `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»'
-make[3]: Entering directory `/«PKGBUILDDIR»'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»'
-make[3]: Entering directory `/«PKGBUILDDIR»/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[3]: Entering directory `/«PKGBUILDDIR»/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»'
-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 `/«PKGBUILDDIR»/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=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/«PKGBUILDDIR»/examples'
-touch debian/stamp-makefile-check
+dh build --parallel
+ dh_testdir -O--parallel
+ dh_auto_configure -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a \
+ CFLAGS="$(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/x86_64-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 bamtk.o bamtk.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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
+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/x86_64-linux-gnu/libhts.a -lhts -lcurse [...]
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -g -O2 -fstack-protector-strong -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 -fstack-protector-strong -Wformat -Werror=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 -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -g -O2 -fstack-protector-strong -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 -fstack-protector-strong -Wformat -Werror=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 -fstack-protector-strong -Wformat -Werror=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 -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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 -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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 -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=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/x86_64-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/x86_64-linux-gnu/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j1 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-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/BddoP4EvN2/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/BddoP4EvN2/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/BddoP4EvN2/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /tmp/BddoP4EvN2/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/BddoP4EvN2/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/BddoP4EvN2/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/BddoP4EvN2/mpileup.bam.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/BddoP4EvN2/mpileup.cram.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/BddoP4EvN2/mpileup.bam.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/BddoP4EvN2/mpileup.cram.list -f /tmp/BddoP4EvN2/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/BddoP4EvN2/mpileup.cram.list -f /tmp/BddoP4EvN2/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/BddoP4EvN2/mpileup.cram.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:1050-1060 /tmp/BddoP4EvN2/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:1050-1060 /tmp/BddoP4EvN2/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/BddoP4EvN2/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/BddoP4EvN2/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/BddoP4EvN2/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/BddoP4EvN2/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/BddoP4EvN2/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/BddoP4EvN2/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (SAM input).. ok
+
+ 56: Count -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (BAM input).. ok
+
+ 58: Count -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 60: Count -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (SAM input).. ok
+
+ 62: Count -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (BAM input).. ok
+
+ 64: Count -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (CRAM input).. ok
+
+ 66: Count -r grp2 -R /tmp/BddoP4EvN2/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/BddoP4EvN2/view.test067.sam -h -l Library 2 /tmp/BddoP4EvN2/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/BddoP4EvN2/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/BddoP4EvN2/view.test069.sam -h -l Library 2 /tmp/BddoP4EvN2/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/BddoP4EvN2/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/BddoP4EvN2/view.test071.sam -h -l Library 2 /tmp/BddoP4EvN2/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/BddoP4EvN2/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/BddoP4EvN2/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/BddoP4EvN2/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/BddoP4EvN2/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/BddoP4EvN2/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: 22576 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/9DPBsRA8JA
+
+.. 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/qFPGXMuTXZ - /«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
-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 /«PKGBUILDDIR»/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /«PKGBUILDDIR»/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|' /«PKGBUILDDIR»/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 --parallel
+ dh_testroot -O--parallel
+ dh_prep -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/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a
+ install -d debian/samtools
+ install -d debian/samtools-test
+ make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-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 -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/
+ install -d debian/samtools-test/usr/share/samtools
+ cp -a ./test debian/samtools-test/usr/share/samtools/
+ dh_installdocs -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
+ install -g 0 -o 0 -d debian/samtools-test/usr/share/doc/samtools-test
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright
+ dh_installchangelogs -O--parallel
+ install -o 0 -g 0 -p -m644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian
+ dh_installman -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 -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
+ (grep -s -v perl:Depends debian/samtools-test.substvars; echo perl:Depends=perl) > debian/samtools-test.substvars.new
+ mv debian/samtools-test.substvars.new debian/samtools-test.substvars
+ dh_link -O--parallel
+ dh_compress -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»'
+ cd debian/samtools-test
+ chmod a-x usr/share/doc/samtools-test/changelog.Debian
+ gzip -9nf usr/share/doc/samtools-test/changelog.Debian
+ cd '/«PKGBUILDDIR»'
+ dh_fixperms -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-linux-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
+ find debian/samtools-test -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/samtools-test ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/samtools-test/usr/share/doc -type f ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/samtools-test/usr/share/man debian/samtools-test/usr/man/ debian/samtools-test/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test -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-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/samtools-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools-test/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
+ dh_strip -O--parallel
+ 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/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ 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-short
+ dh_makeshlibs -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ rm -f debian/samtools-test/DEBIAN/shlibs
+ dh_shlibdeps -O--parallel
+ install -o 0 -g 0 -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa were not linked against libhts.so.1 (they use none of the library's symbols)
+ install -o 0 -g 0 -d debian/samtools-test/DEBIAN
+ dh_installdeb -O--parallel
+ dh_gencontrol -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_amd64.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_amd64.deb'.
- dpkg-genchanges >../samtools_0.1.19-1_amd64.changes
+ chmod 644 debian/samtools/DEBIAN/control
+ chown 0:0 debian/samtools/DEBIAN/control
+ echo misc:Depends= >> debian/samtools-test.substvars
+ dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -Pdebian/samtools-test
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools-test: unused substitution variable ${perl:Depends}
+ chmod 644 debian/samtools-test/DEBIAN/control
+ chown 0:0 debian/samtools-test/DEBIAN/control
+ dh_md5sums -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
+ (cd debian/samtools-test >/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-test/DEBIAN/md5sums
+ chown 0:0 debian/samtools-test/DEBIAN/md5sums
+ dh_builddeb -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package `samtools' in `../samtools_1.1-1_amd64.deb'.
+ dpkg-deb --build debian/samtools-test ..
+dpkg-deb: building package `samtools-test' in `../samtools-test_1.1-1_all.deb'.
+ dpkg-genchanges >../samtools_1.1-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build samtools-0.1.19
-dpkg-source: info: unapplying fix_coverage_cap.patch
-dpkg-source: info: unapplying fix_segfault_with_small_ref.patch
-dpkg-source: info: unapplying fix_example_makefile.patch
+ dpkg-source --after-build samtools-1.1
+dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-1734
+Build finished at 20140925-0908
Finished
────────
@@ -637,84 +1444,314 @@ Finished
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+lintian
+───────
+
+Merged Build-Depends: lintian
+Filtered Build-Depends: lintian
+dpkg-deb: building package `sbuild-build-depends-lintian-dummy' in `/«BUILDDIR»/resolver-jRfKH3/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
+OK
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install lintian build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ diffstat hardening-includes libapt-pkg-perl libarchive-zip-perl
+ libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl
+ libfile-basedir-perl libio-pty-perl libio-socket-inet6-perl
+ libio-socket-ssl-perl libio-string-perl libipc-run-perl
+ liblist-moreutils-perl libmailtools-perl libnet-dns-perl
+ libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
+ libnet-ssleay-perl libparse-debianchangelog-perl libsocket6-perl libssl1.0.0
+ libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
+ patchutils t1utils
+Suggested packages:
+ ca-certificates libhtml-parser-perl libhtml-template-perl libxml-simple-perl
+ libwww-perl binutils-multiarch libyaml-perl
+Recommended packages:
+ libauthen-sasl-perl libperlio-gzip-perl ifupdown
+The following NEW packages will be installed:
+ diffstat hardening-includes libapt-pkg-perl libarchive-zip-perl
+ libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl
+ libfile-basedir-perl libio-pty-perl libio-socket-inet6-perl
+ libio-socket-ssl-perl libio-string-perl libipc-run-perl
+ liblist-moreutils-perl libmailtools-perl libnet-dns-perl
+ libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
+ libnet-ssleay-perl libparse-debianchangelog-perl libsocket6-perl libssl1.0.0
+ libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
+ patchutils sbuild-build-depends-lintian-dummy t1utils
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/3597 kB of archives.
+After this operation, 12.0 MB of additional disk space will be used.
+Selecting previously unselected package libssl1.0.0:amd64.
+(Reading database ... 13304 files and directories currently installed.)
+Preparing to unpack .../libssl1.0.0_1.0.1i-2_amd64.deb ...
+Unpacking libssl1.0.0:amd64 (1.0.1i-2) ...
+Selecting previously unselected package netbase.
+Preparing to unpack .../archives/netbase_5.2_all.deb ...
+Unpacking netbase (5.2) ...
+Selecting previously unselected package diffstat.
+Preparing to unpack .../diffstat_1.58-1_amd64.deb ...
+Unpacking diffstat (1.58-1) ...
+Selecting previously unselected package hardening-includes.
+Preparing to unpack .../hardening-includes_2.5+nmu1_all.deb ...
+Unpacking hardening-includes (2.5+nmu1) ...
+Selecting previously unselected package libapt-pkg-perl.
+Preparing to unpack .../libapt-pkg-perl_0.1.29+b2_amd64.deb ...
+Unpacking libapt-pkg-perl (0.1.29+b2) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.38-1_all.deb ...
+Unpacking libarchive-zip-perl (1.38-1) ...
+Selecting previously unselected package libsub-name-perl.
+Preparing to unpack .../libsub-name-perl_0.07-1+b1_amd64.deb ...
+Unpacking libsub-name-perl (0.07-1+b1) ...
+Selecting previously unselected package libclass-accessor-perl.
+Preparing to unpack .../libclass-accessor-perl_0.34-1_all.deb ...
+Unpacking libclass-accessor-perl (0.34-1) ...
+Selecting previously unselected package libclone-perl.
+Preparing to unpack .../libclone-perl_0.37-1+b1_amd64.deb ...
+Unpacking libclone-perl (0.37-1+b1) ...
+Selecting previously unselected package libdigest-hmac-perl.
+Preparing to unpack .../libdigest-hmac-perl_1.03+dfsg-1_all.deb ...
+Unpacking libdigest-hmac-perl (1.03+dfsg-1) ...
+Selecting previously unselected package libnet-ssleay-perl.
+Preparing to unpack .../libnet-ssleay-perl_1.65-1+b1_amd64.deb ...
+Unpacking libnet-ssleay-perl (1.65-1+b1) ...
+Selecting previously unselected package libio-socket-ssl-perl.
+Preparing to unpack .../libio-socket-ssl-perl_1.998-1_all.deb ...
+Unpacking libio-socket-ssl-perl (1.998-1) ...
+Selecting previously unselected package libnet-smtp-ssl-perl.
+Preparing to unpack .../libnet-smtp-ssl-perl_1.01-3_all.deb ...
+Unpacking libnet-smtp-ssl-perl (1.01-3) ...
+Selecting previously unselected package libmailtools-perl.
+Preparing to unpack .../libmailtools-perl_2.13-1_all.deb ...
+Unpacking libmailtools-perl (2.13-1) ...
+Selecting previously unselected package libsocket6-perl.
+Preparing to unpack .../libsocket6-perl_0.25-1+b1_amd64.deb ...
+Unpacking libsocket6-perl (0.25-1+b1) ...
+Selecting previously unselected package libio-socket-inet6-perl.
+Preparing to unpack .../libio-socket-inet6-perl_2.72-1_all.deb ...
+Unpacking libio-socket-inet6-perl (2.72-1) ...
+Selecting previously unselected package libnet-ip-perl.
+Preparing to unpack .../libnet-ip-perl_1.26-1_all.deb ...
+Unpacking libnet-ip-perl (1.26-1) ...
+Selecting previously unselected package libnet-dns-perl.
+Preparing to unpack .../libnet-dns-perl_0.79-2_amd64.deb ...
+Unpacking libnet-dns-perl (0.79-2) ...
+Selecting previously unselected package libnet-domain-tld-perl.
+Preparing to unpack .../libnet-domain-tld-perl_1.72-1_all.deb ...
+Unpacking libnet-domain-tld-perl (1.72-1) ...
+Selecting previously unselected package libemail-valid-perl.
+Preparing to unpack .../libemail-valid-perl_1.195-1_all.deb ...
+Unpacking libemail-valid-perl (1.195-1) ...
+Selecting previously unselected package libfile-basedir-perl.
+Preparing to unpack .../libfile-basedir-perl_0.03-1_all.deb ...
+Unpacking libfile-basedir-perl (0.03-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_amd64.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Selecting previously unselected package libio-string-perl.
+Preparing to unpack .../libio-string-perl_1.08-3_all.deb ...
+Unpacking libio-string-perl (1.08-3) ...
+Selecting previously unselected package libipc-run-perl.
+Preparing to unpack .../libipc-run-perl_0.92-1_all.deb ...
+Unpacking libipc-run-perl (0.92-1) ...
+Selecting previously unselected package liblist-moreutils-perl.
+Preparing to unpack .../liblist-moreutils-perl_0.33-2+b1_amd64.deb ...
+Unpacking liblist-moreutils-perl (0.33-2+b1) ...
+Selecting previously unselected package libparse-debianchangelog-perl.
+Preparing to unpack .../libparse-debianchangelog-perl_1.2.0-1.1_all.deb ...
+Unpacking libparse-debianchangelog-perl (1.2.0-1.1) ...
+Selecting previously unselected package libtext-levenshtein-perl.
+Preparing to unpack .../libtext-levenshtein-perl_0.09-1_all.deb ...
+Unpacking libtext-levenshtein-perl (0.09-1) ...
+Selecting previously unselected package liburi-perl.
+Preparing to unpack .../liburi-perl_1.64-1_all.deb ...
+Unpacking liburi-perl (1.64-1) ...
+Selecting previously unselected package patchutils.
+Preparing to unpack .../patchutils_0.3.3-1_amd64.deb ...
+Unpacking patchutils (0.3.3-1) ...
+Selecting previously unselected package t1utils.
+Preparing to unpack .../t1utils_1.37-2.1_amd64.deb ...
+Unpacking t1utils (1.37-2.1) ...
+Selecting previously unselected package lintian.
+Preparing to unpack .../lintian_2.5.27_all.deb ...
+Unpacking lintian (2.5.27) ...
+Selecting previously unselected package sbuild-build-depends-lintian-dummy.
+Preparing to unpack .../sbuild-build-depends-lintian-dummy.deb ...
+Unpacking sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Processing triggers for man-db (2.7.0.1-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libssl1.0.0:amd64 (1.0.1i-2) ...
+Setting up netbase (5.2) ...
+Setting up diffstat (1.58-1) ...
+Setting up hardening-includes (2.5+nmu1) ...
+Setting up libapt-pkg-perl (0.1.29+b2) ...
+Setting up libarchive-zip-perl (1.38-1) ...
+Setting up libsub-name-perl (0.07-1+b1) ...
+Setting up libclass-accessor-perl (0.34-1) ...
+Setting up libclone-perl (0.37-1+b1) ...
+Setting up libdigest-hmac-perl (1.03+dfsg-1) ...
+Setting up libnet-ssleay-perl (1.65-1+b1) ...
+Setting up libio-socket-ssl-perl (1.998-1) ...
+Setting up libnet-smtp-ssl-perl (1.01-3) ...
+Setting up libmailtools-perl (2.13-1) ...
+Setting up libsocket6-perl (0.25-1+b1) ...
+Setting up libio-socket-inet6-perl (2.72-1) ...
+Setting up libnet-ip-perl (1.26-1) ...
+Setting up libnet-dns-perl (0.79-2) ...
+Setting up libnet-domain-tld-perl (1.72-1) ...
+Setting up libemail-valid-perl (1.195-1) ...
+Setting up libfile-basedir-perl (0.03-1) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libio-string-perl (1.08-3) ...
+Setting up libipc-run-perl (0.92-1) ...
+Setting up liblist-moreutils-perl (0.33-2+b1) ...
+Setting up libparse-debianchangelog-perl (1.2.0-1.1) ...
+Setting up libtext-levenshtein-perl (0.09-1) ...
+Setting up liburi-perl (1.64-1) ...
+Setting up patchutils (0.3.3-1) ...
+Setting up t1utils (1.37-2.1) ...
+Setting up lintian (2.5.27) ...
+Setting up sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-11) ...
+I: samtools source: quilt-patch-using-template-description debian-changes
+W: samtools source: newer-standards-version 3.9.6 (current is 3.9.5)
+P: samtools source: debian-watch-may-check-gpg-signature
+P: samtools-test: no-upstream-changelog
+I: samtools-test: description-synopsis-might-not-be-phrased-properly
+P: samtools: no-upstream-changelog
+W: samtools: script-with-language-extension usr/bin/blast2sam.pl
+W: samtools: script-with-language-extension usr/bin/bowtie2sam.pl
+W: samtools: script-with-language-extension usr/bin/export2sam.pl
+W: samtools: script-with-language-extension usr/bin/interpolate_sam.pl
+W: samtools: script-with-language-extension usr/bin/novo2sam.pl
+W: samtools: script-with-language-extension usr/bin/psl2sam.pl
+W: samtools: script-with-language-extension usr/bin/sam2vcf.pl
+W: samtools: script-with-language-extension usr/bin/samtools.pl
+W: samtools: script-with-language-extension usr/bin/seq_cache_populate.pl
+W: samtools: script-with-language-extension usr/bin/soap2sam.pl
+W: samtools: script-with-language-extension usr/bin/varfilter.py
+W: samtools: script-with-language-extension usr/bin/wgsim_eval.pl
+W: samtools: script-with-language-extension usr/bin/zoom2sam.pl
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:30
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:32
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:46
+I: samtools: spelling-error-in-manpage usr/share/man/man1/samtools.1.gz allows to allows one to
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:144
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:171
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:174
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:433
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:605
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:741
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:911
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz 16 more occurrences not shown
+W: samtools: binary-without-manpage usr/bin/ace2sam
+W: samtools: binary-without-manpage usr/bin/blast2sam.pl
+W: samtools: binary-without-manpage usr/bin/bowtie2sam.pl
+W: samtools: binary-without-manpage usr/bin/export2sam.pl
+W: samtools: binary-without-manpage usr/bin/interpolate_sam.pl
+W: samtools: binary-without-manpage usr/bin/maq2sam-long
+W: samtools: binary-without-manpage usr/bin/maq2sam-short
+W: samtools: binary-without-manpage usr/bin/md5fa
+W: samtools: binary-without-manpage usr/bin/md5sum-lite
+W: samtools: binary-without-manpage usr/bin/novo2sam.pl
+W: samtools: binary-without-manpage usr/bin/plot-bamstats
+W: samtools: binary-without-manpage usr/bin/psl2sam.pl
+W: samtools: binary-without-manpage usr/bin/sam2vcf.pl
+W: samtools: binary-without-manpage usr/bin/samtools.pl
+W: samtools: binary-without-manpage usr/bin/seq_cache_populate.pl
+W: samtools: binary-without-manpage usr/bin/soap2sam.pl
+W: samtools: binary-without-manpage usr/bin/varfilter.py
+W: samtools: binary-without-manpage usr/bin/wgsim
+W: samtools: binary-without-manpage usr/bin/wgsim_eval.pl
+W: samtools: binary-without-manpage usr/bin/zoom2sam.pl
+
+I: Lintian run was successful.
+
+┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.19-1_amd64.changes:
-────────────────────────────────
+samtools_1.1-1_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
-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.
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- 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).
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.19-1_amd64.deb
-───────────────────────────
+samtools_1.1-1_amd64.deb
+────────────────────────
new debian package, version 2.0.
- size 562956 bytes: control archive=1928 bytes.
- 32 bytes, 1 lines conffiles
- 792 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
+ size 378168 bytes: control archive=1555 bytes.
+ 801 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
Package: samtools
- Version: 0.1.19-1
+ Version: 1.1-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1262
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
+ Installed-Size: 1040
+ Depends: libc6 (>= 2.15), 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
@@ -722,110 +1759,298 @@ samtools_0.1.19-1_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 17:34 ./
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-27 06:52 ./etc/bash_completion.d/samtools
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/lib/samtools/
--rwxr-xr-x root/root 18680 2013-03-30 17:34 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 22696 2013-03-30 17:34 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 172720 2013-03-30 17:34 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 10368 2013-03-30 17:34 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10368 2013-03-30 17:34 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 14472 2013-03-30 17:34 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 10320 2013-03-30 17:34 ./usr/lib/samtools/md5sum-lite
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--rwxr-xr-x root/root 154664 2013-03-30 17:34 ./usr/bin/bcftools
--rwxr-xr-x root/root 27032 2013-03-30 17:34 ./usr/bin/razip
--rwxr-xr-x root/root 416672 2013-03-30 17:34 ./usr/bin/samtools
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-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2013-03-30 17:34 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 29649 2013-03-18 23:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 21028 2013-03-18 23:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 2685 2013-03-18 23:43 ./usr/share/samtools/r2plot.lua
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--rwxr-xr-x root/root 2112 2013-03-18 23:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2415 2013-03-18 23:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 15707 2013-03-18 23:43 ./usr/share/samtools/vcfutils.pl
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 17:34 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 17:34 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/samtools/
--rw-r--r-- root/root 10421 2013-03-18 23:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 17:32 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 10421 2013-03-18 23:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2013-03-30 17:34 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 786 2013-03-18 23:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2013-03-18 23:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2013-03-18 23:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2013-03-18 23:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2013-03-18 23:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126580 2013-03-30 17:34 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 5012 2013-03-30 16:03 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2012-01-09 11:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2012-01-09 11:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 916 2013-03-18 23:43 ./usr/share/doc/samtools/AUTHORS
-lrwxrwxrwx root/root 0 2013-03-30 17:34 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_amd64.deb
-─────────────────────────────
+drwxr-xr-x root/root 0 2014-09-25 09:08 ./
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+-rwxr-xr-x root/root 48023 2014-09-20 00:51 ./usr/bin/plot-bamstats
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+-rw-r--r-- root/root 1031 2014-09-25 08:56 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3270 2014-09-25 09:05 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2014-09-25 08:56 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2014-09-25 08:56 ./usr/share/doc/samtools/reference
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+-rw-r--r-- root/root 12774 2014-09-25 09:08 ./usr/share/man/man1/samtools.1.gz
+
+
+samtools-test_1.1-1_all.deb
+───────────────────────────
new debian package, version 2.0.
- size 123276 bytes: control archive=923 bytes.
- 712 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
+ size 2644466 bytes: control archive=6161 bytes.
+ 467 bytes, 14 lines control
+ 17627 bytes, 215 lines md5sums
+ Package: samtools-test
Source: samtools
- Version: 0.1.19-1
- Architecture: amd64
+ Version: 1.1-1
+ Architecture: all
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 404
- Section: libdevel
+ Installed-Size: 9148
+ Section: science
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.
+ Homepage: http://www.htslib.org/
+ Description: test files for the samtools package.
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format.
.
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/include/samtools/
--rw-r--r-- root/root 2688 2013-03-18 23:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2013-03-18 23:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 17815 2013-03-18 23:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 6326 2013-03-18 23:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 25788 2013-03-18 23:43 ./usr/include/samtools/bam.h
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--rw-r--r-- root/root 327050 2013-03-30 17:34 ./usr/lib/libbam.a
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--rw-r--r-- root/root 10421 2013-03-18 23:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 17:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 10421 2013-03-18 23:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5012 2013-03-30 16:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 916 2013-03-18 23:43 ./usr/share/doc/libbam-dev/AUTHORS
+ This package contains test files for the samtools package.
+
+drwxr-xr-x root/root 0 2014-09-25 09:08 ./
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+-rw-r--r-- root/root 3462 2014-09-25 08:56 ./usr/share/doc/samtools-test/copyright
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+-rw-r--r-- root/root 1292 2014-09-20 00:51 ./usr/share/samtools/test/dat/cat.hdr
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+-rw-r--r-- root/root 57 2014-09-20 00:51 ./usr/share/samtools/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
+-rw-r--r-- root/root 61 2014-09-20 00:51 ./usr/share/samtools/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
+-rw-r--r-- root/root 36 2014-09-20 00:51 ./usr/share/samtools/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
+-rw-r--r-- root/root 31 2014-09-20 00:51 ./usr/share/samtools/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
+-rw-r--r-- root/root 42 2014-09-20 00:51 ./usr/share/samtools/test/dat/depad.001.fa
+-rw-r--r-- root/root 16 2014-09-20 00:51 ./usr/share/samtools/test/dat/depad.001.fa.fai
+-rw-r--r-- root/root 7908 2014-09-20 00:51 ./usr/share/samtools/test/dat/depad.001p.sam
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+-rw-r--r-- root/root 5090 2014-09-20 00:51 ./usr/share/samtools/test/dat/large_chrom.sam
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+-rw-r--r-- root/root 351091 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.1.sam
+-rw-r--r-- root/root 104866 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.2.sam
+-rw-r--r-- root/root 105843 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.3.sam
+-rw-r--r-- root/root 78 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.err.1
+-rw-r--r-- root/root 2716 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.out.1
+-rw-r--r-- root/root 81484 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.out.2
+-rw-r--r-- root/root 295 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.out.3
+-rw-r--r-- root/root 113722 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.out.4
+-rw-r--r-- root/root 4284 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.ref.fa
+-rw-r--r-- root/root 17 2014-09-20 00:51 ./usr/share/samtools/test/dat/mpileup.ref.fa.fai
+-rw-r--r-- root/root 758 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_a.bam
+-rw-r--r-- root/root 264 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_a.bam.bai
+-rw-r--r-- root/root 1429 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_a.sam
+-rw-r--r-- root/root 687 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_b.bam
+-rw-r--r-- root/root 192 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_b.bam.bai
+-rw-r--r-- root/root 1252 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_b.sam
+-rw-r--r-- root/root 655 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_c.bam
+-rw-r--r-- root/root 176 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_c.bam.bai
+-rw-r--r-- root/root 1253 2014-09-20 00:51 ./usr/share/samtools/test/dat/test_input_1_c.sam
+-rw-r--r-- root/root 1335 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.001.01.bed
+-rw-r--r-- root/root 1134 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.001.02.bed
+-rw-r--r-- root/root 130 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.001.fa
+-rw-r--r-- root/root 33 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.001.fa.fai
+-rw-r--r-- root/root 5073 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.001.sam
+-rw-r--r-- root/root 1313 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.002.01.bed
+-rw-r--r-- root/root 1302 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.002.02.bed
+-rw-r--r-- root/root 64 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.002.fa
+-rw-r--r-- root/root 13 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.002.fa.fai
+-rw-r--r-- root/root 3692 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.002.sam
+-rw-r--r-- root/root 2142 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.003.expected.sam
+-rw-r--r-- root/root 2224 2014-09-20 00:51 ./usr/share/samtools/test/dat/view.003.sam
+drwxr-xr-x root/root 0 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/
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+-rw-r--r-- root/root 0 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected
+-rw-r--r-- root/root 82 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected.err
+-rw-r--r-- root/root 1047 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam
+-rw-r--r-- root/root 1102 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam.expected
+-rw-r--r-- root/root 715 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam
+-rw-r--r-- root/root 715 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam.expected
+-rw-r--r-- root/root 715 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam
+-rw-r--r-- root/root 715 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam.expected
+-rw-r--r-- root/root 715 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/5_ct.sam
+-rw-r--r-- root/root 735 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/5_ct.sam.expected
+-rw-r--r-- root/root 735 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/6_ct_replace.sam
+-rw-r--r-- root/root 735 2014-09-20 00:51 ./usr/share/samtools/test/fixmate/6_ct_replace.sam.expected
+drwxr-xr-x root/root 0 2014-09-20 00:51 ./usr/share/samtools/test/idxstats/
+-rw-r--r-- root/root 58 2014-09-20 00:51 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected
+-rw-r--r-- root/root 0 2014-09-20 00:51 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected.err
+drwxr-xr-x root/root 0 2014-09-25 09:08 ./usr/share/samtools/test/merge/
+-rw-r--r-- root/root 1181 2014-09-20 00:51 ./usr/share/samtools/test/merge/2.merge.expected.bam
+-rw-r--r-- root/root 1199 2014-09-20 00:51 ./usr/share/samtools/test/merge/3.merge.expected.bam
+-rw-r--r-- root/root 525 2014-09-20 00:51 ./usr/share/samtools/test/merge/3.merge.expected.err
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+-rw-r--r-- root/root 15673 2014-09-20 00:51 ./usr/share/samtools/test/merge/test_bam_translate.c
+-rw-r--r-- root/root 184 2014-09-20 00:51 ./usr/share/samtools/test/merge/test_header.sam
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┌──────────────────────────────────────────────────────────────────────────────┐
@@ -833,55 +2058,131 @@ drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/libbam-dev/
└──────────────────────────────────────────────────────────────────────────────┘
-lintian
-───────
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-P: samtools source: unneeded-build-dep-on-quilt
-W: samtools: duplicate-changelog-files usr/share/doc/samtools/NEWS.gz usr/share/doc/samtools/changelog.gz
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:9
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:23
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:25
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:33
-I: samtools: spelling-error-in-manpage usr/share/man/man1/samtools.1.gz allows to allows one to
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-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:59
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-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:322
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-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:356
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz 30 more occurrences not shown
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-
-I: Lintian run was successful.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
-Not cleaning session: cloned chroot in use
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
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+ gettext-base* groff-base* hardening-includes* intltool-debian*
+ libapt-pkg-perl* libarchive-zip-perl* libasprintf0c2*
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+ libio-socket-ssl-perl* libio-string-perl* libipc-run-perl*
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+ libpipeline1* libsocket6-perl* libssl1.0.0* libsub-name-perl*
+ libtext-levenshtein-perl* libtinfo-dev* libunistring0* liburi-perl* libxml2*
+ lintian* man-db* netbase* patchutils* po-debconf*
+ sbuild-build-depends-core-dummy* sbuild-build-depends-lintian-dummy*
+ sbuild-build-depends-samtools-dummy* t1utils* tabix* zlib1g-dev*
+0 upgraded, 0 newly installed, 58 to remove and 0 not upgraded.
+After this operation, 43.6 MB disk space will be freed.
+(Reading database ... 14528 files and directories currently installed.)
+Removing sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Removing bash-completion (1:2.1-4) ...
+Purging configuration files for bash-completion (1:2.1-4) ...
+Removing sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Removing lintian (2.5.27) ...
+Purging configuration files for lintian (2.5.27) ...
+Removing debhelper (9.20140817) ...
+Removing man-db (2.7.0.1-1) ...
+Purging configuration files for man-db (2.7.0.1-1) ...
+Removing bsdmainutils (9.0.5) ...
+Purging configuration files for bsdmainutils (9.0.5) ...
+Removing diffstat (1.58-1) ...
+Removing file (1:5.19-2) ...
+Removing po-debconf (1.0.16+nmu3) ...
+Removing intltool-debian (0.35.0+20060710.1) ...
+Removing gettext (0.19.2-2) ...
+Removing gettext-base (0.19.2-2) ...
+Removing groff-base (1.22.2-8) ...
+Purging configuration files for groff-base (1.22.2-8) ...
+Removing hardening-includes (2.5+nmu1) ...
+Removing libapt-pkg-perl (0.1.29+b2) ...
+Removing libarchive-zip-perl (1.38-1) ...
+Removing libasprintf0c2:amd64 (0.19.2-2) ...
+Removing libparse-debianchangelog-perl (1.2.0-1.1) ...
+Removing libclass-accessor-perl (0.34-1) ...
+Removing libclone-perl (0.37-1+b1) ...
+Removing libcroco3:amd64 (0.6.8-3) ...
+Purging configuration files for libcroco3:amd64 (0.6.8-3) ...
+Removing libemail-valid-perl (1.195-1) ...
+Removing libnet-dns-perl (0.79-2) ...
+Removing libdigest-hmac-perl (1.03+dfsg-1) ...
+Removing libglib2.0-0:amd64 (2.42.0-1) ...
+Purging configuration files for libglib2.0-0:amd64 (2.42.0-1) ...
+Removing libffi6:amd64 (3.1-2) ...
+Purging configuration files for libffi6:amd64 (3.1-2) ...
+Removing libfile-basedir-perl (0.03-1) ...
+Removing libhts-dev:amd64 (1.1-1) ...
+Removing libhts1:amd64 (1.1-1) ...
+Purging configuration files for libhts1:amd64 (1.1-1) ...
+Removing libipc-run-perl (0.92-1) ...
+Removing libio-pty-perl (1:1.08-1+b4) ...
+Removing libio-socket-inet6-perl (2.72-1) ...
+Removing libmailtools-perl (2.13-1) ...
+Removing libnet-smtp-ssl-perl (1.01-3) ...
+Removing libio-socket-ssl-perl (1.998-1) ...
+Removing libio-string-perl (1.08-3) ...
+Removing liblist-moreutils-perl (0.33-2+b1) ...
+Removing libmagic1:amd64 (1:5.19-2) ...
+Purging configuration files for libmagic1:amd64 (1:5.19-2) ...
+Removing libncurses5-dev:amd64 (5.9+20140913-1) ...
+Removing libnet-domain-tld-perl (1.72-1) ...
+Removing libnet-ip-perl (1.26-1) ...
+Removing libnet-ssleay-perl (1.65-1+b1) ...
+Removing libpipeline1:amd64 (1.3.1-1) ...
+Purging configuration files for libpipeline1:amd64 (1.3.1-1) ...
+Removing libsocket6-perl (0.25-1+b1) ...
+Removing libssl1.0.0:amd64 (1.0.1i-2) ...
+Purging configuration files for libssl1.0.0:amd64 (1.0.1i-2) ...
+Removing libsub-name-perl (0.07-1+b1) ...
+Removing libtext-levenshtein-perl (0.09-1) ...
+Removing libtinfo-dev:amd64 (5.9+20140913-1) ...
+Removing libunistring0:amd64 (0.9.3-5.2) ...
+Purging configuration files for libunistring0:amd64 (0.9.3-5.2) ...
+Removing liburi-perl (1.64-1) ...
+Removing libxml2:amd64 (2.9.1+dfsg1-4) ...
+Purging configuration files for libxml2:amd64 (2.9.1+dfsg1-4) ...
+Removing netbase (5.2) ...
+Purging configuration files for netbase (5.2) ...
+Removing patchutils (0.3.3-1) ...
+Removing sbuild-build-depends-core-dummy (0.invalid.0) ...
+Removing t1utils (1.37-2.1) ...
+Removing tabix (1.1-1) ...
+Removing zlib1g-dev:amd64 (1:1.2.8.dfsg-2) ...
+Processing triggers for libc-bin (2.19-11) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: amd64
-Build-Space: 16868
-Build-Time: 50
+Build-Space: 32068
+Build-Time: 128
Distribution: unstable
Host Architecture: amd64
-Install-Time: 34
-Job: samtools_0.1.19-1.dsc
+Install-Time: 15
+Job: samtools_1.1-1.dsc
Lintian: pass
Machine Architecture: amd64
Package: samtools
-Package-Time: 89
-Source-Version: 0.1.19-1
-Space: 16868
+Package-Time: 151
+Source-Version: 1.1-1
+Space: 32068
Status: successful
-Version: 0.1.19-1
+Version: 1.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-1734
-Build needed 00:01:29, 16868k disc space
+Finished at 20140925-0908
+Build needed 00:02:31, 32068k disc space
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git
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