[med-svn] [bedtools] 01/01: bedtools (2.25.0-1) unstable; urgency=medium
Charles Plessy
plessy at moszumanska.debian.org
Sat Sep 5 06:12:36 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch meta
in repository bedtools.
commit 5dfbed5e01b209252b8790bb4acfdcd1d952f441
Author: Charles Plessy <plessy at debian.org>
Date: Sat Sep 5 08:11:55 2015 +0200
bedtools (2.25.0-1) unstable; urgency=medium
e37865 Merge tag 'v2.25.0' into debian/unstable
-- Charles Plessy <plessy at debian.org> Fri, 04 Sep 2015 16:55:21 +0200
---
amd64.changes | 82 +-
amd64.log | 4306 +++++++++++++++++++++++++++++++++++++++++----------------
dsc | 60 +-
upload | 14 +-
4 files changed, 3219 insertions(+), 1243 deletions(-)
diff --git a/amd64.changes b/amd64.changes
index fd74dad..26263ac 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,63 +2,55 @@
Hash: SHA512
Format: 1.8
-Date: Fri, 21 Mar 2014 14:51:44 +0900
+Date: Fri, 04 Sep 2015 16:55:21 +0200
Source: bedtools
Binary: bedtools bedtools-test
Architecture: source all amd64
-Version: 2.19.1-1
+Version: 2.25.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
-Description:
+Description:
bedtools - suite of utilities for comparing genomic features
bedtools-test - test data for the bedtools package
-Changes:
- bedtools (2.19.1-1) unstable; urgency=medium
+Changes:
+ bedtools (2.25.0-1) unstable; urgency=medium
.
- 479e63b Merge tag 'v2.19.1' into debian/unstable
- .
- [ Charles Plessy ]
- 93a7cf1 Create autopkgtest testsuite and a new package bedtools-test.
- 46183f8 debian/copyright: update path, correct license short name.
- 4fd441a debian/rules: removed obsolete exception of compression.
- .
- [ James McCoy ]
- b4fa8e1 Move debian/upstream to debian/upstream/metadata
-Checksums-Sha1:
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- 534c0241d3885bf1c0c8251996f6119d4a6f6a16 4150267 bedtools_2.19.1.orig.tar.gz
- a8db88b12970fccadf84d0e1a35e24ff4dc103c8 8664 bedtools_2.19.1-1.debian.tar.xz
- 38b8fc819b73674cacfacf01b88cf8b8f6e7b73c 2400684 bedtools-test_2.19.1-1_all.deb
- 8da42ee9f8daa34777a1b89d8e06f0c3ab5f1d5b 526828 bedtools_2.19.1-1_amd64.deb
-Checksums-Sha256:
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- c7df72aa54af8dd5b50837c53432070bcb0b82d480c0e791163e1a00b66ced1e 4150267 bedtools_2.19.1.orig.tar.gz
- 8b73a1d629c335070ac3266b98127a87ddb2c9dd2463621195f2fa724f0a3cd6 8664 bedtools_2.19.1-1.debian.tar.xz
- 6a4e5c6282ea8482f4294b02f26c81f7f2f6f291f03db282671bfc819e9478a9 2400684 bedtools-test_2.19.1-1_all.deb
- 6e99c5fc2f5b72730547106f17a639d78ec27e47246a82da6ebc59bdc795e46b 526828 bedtools_2.19.1-1_amd64.deb
-Files:
- 131467932a1e5cfd35bd0d9ae75cbb4c 2027 science optional bedtools_2.19.1-1.dsc
- 98c549049c44ce39d58e63e152b99566 4150267 science optional bedtools_2.19.1.orig.tar.gz
- c7ef7e2d73a30d4c753d87a60aea8aa6 8664 science optional bedtools_2.19.1-1.debian.tar.xz
- 40254590ad8e7135a68767fa3cf39e56 2400684 science optional bedtools-test_2.19.1-1_all.deb
- 176a81ad2b3bed0ccf58b5478d451b0f 526828 science optional bedtools_2.19.1-1_amd64.deb
+ e37865 Merge tag 'v2.25.0' into debian/unstable
+Checksums-Sha1:
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+ 949fedcacc2e68adfd45e2034d20c3a432b3f2ad 19586049 bedtools_2.25.0.orig.tar.gz
+ ea7804ab77a2d816ef77b35d62396bebf9ec96ba 8132 bedtools_2.25.0-1.debian.tar.xz
+ c419dc06dca83db6c455663177685b7f8455de53 10195822 bedtools-test_2.25.0-1_all.deb
+ 1666aaa0b44f4bffb0c52c08ef038c45ba318d9a 574390 bedtools_2.25.0-1_amd64.deb
+Checksums-Sha256:
+ 0061c97c6b9595a95f573eeba6811ec3e3fd62209226c8020e7d7165e373e59b 2071 bedtools_2.25.0-1.dsc
+ 159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb 19586049 bedtools_2.25.0.orig.tar.gz
+ 5eaa3670f4ae5fbd83d731e88e8f64c4546c8fef341751856c3d02b6b11c1327 8132 bedtools_2.25.0-1.debian.tar.xz
+ 3925ee6778bd6798b31ed8df35dbf67a3d738436f6a7ef071c8dc1285f6fbd94 10195822 bedtools-test_2.25.0-1_all.deb
+ cae27740683d8a178d9bf565d01b016115125b9442cea7781be9fcd8e97accbb 574390 bedtools_2.25.0-1_amd64.deb
+Files:
+ fb15306ca95d99168ec823af0676eed3 2071 science optional bedtools_2.25.0-1.dsc
+ 534fb4a7bf0d0c3f05be52a0160d8e3d 19586049 science optional bedtools_2.25.0.orig.tar.gz
+ ac63b2b87d982493ca837e6b6ad6431c 8132 science optional bedtools_2.25.0-1.debian.tar.xz
+ 2e1dbe5447a8bd1633fbc7809bcd0e2f 10195822 science optional bedtools-test_2.25.0-1_all.deb
+ 15a2df0c0fd8033b82f9a1bb11966f42 574390 science optional bedtools_2.25.0-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index b9b15ba..2cad221 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,30 +1,30 @@
-sbuild (Debian sbuild) 0.64.1 (13 Oct 2013) on aqwa.igloo
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bubu.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.19.1-1 (amd64) 21 mars 2014 14:54 ║
+║ bedtools 2.25.0-1 (amd64) 04 sept. 2015 17:11 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.19.1-1
-Source Version: 2.19.1-1
+Version: 2.25.0-1
+Source Version: 2.25.0-1
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/bedtools-v7J737/bedtools-2.19.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/bedtools-v7J737' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-23307417-a3f6-4624-bcca-ffa4855c0f92' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/bedtools-lcTzss/bedtools-2.25.0' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bedtools-lcTzss' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-89a3befd-5ba5-4c3b-b1f0-5c82865b0520' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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]
-Hit http://ftp.jp.debian.org unstable/main Translation-en/DiffIndex
-Fetched 15.8 kB in 2s (6000 B/s)
+Hit http://ftp2.jp.debian.org sid InRelease
+Get:1 http://ftp2.jp.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:2 http://ftp2.jp.debian.org sid/main amd64 Packages/DiffIndex [7876 B]
+Get:3 http://ftp2.jp.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Fetched 23.6 kB in 2s (9595 B/s)
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -39,15 +39,24 @@ Reading state information...
Local sources
─────────────
-bedtools_2.19.1-1.dsc exists in .; copying to chroot
+bedtools_2.25.0-1.dsc exists in .; copying to chroot
-Check arch
-──────────
+Check architectures
+───────────────────
+
+
+Check dependencies
+──────────────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-Lepc5Y/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-WqfW0b/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -62,17 +71,22 @@ 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/820 B of archives.
+Need to get 0 B/776 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 ... 11224 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), cdbs, debhelper (>= 9), quilt, python, 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), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-WzBuah/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11859 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), python, zlib1g-dev, samtools
+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 (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), python, zlib1g-dev, samtools
+dpkg-deb: building package 'sbuild-build-depends-bedtools-dummy' in '/«BUILDDIR»/resolver-mLmSiH/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,186 +98,180 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libglib2.0-0
- libmagic1 libncursesw5 libpipeline1 libpython-stdlib libpython2.7-minimal
+ bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian
+ libasprintf0v5 libcroco3 libexpat1 libffi6 libglib2.0-0 libhts1 libicu55
+ libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
- quilt zlib1g-dev
+ samtools zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl python-doc python-tk python2.7-doc
- binfmt-support procmail graphviz default-mta mail-transport-agent
+ wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
+ libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info libgpm2 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:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libglib2.0-0
- libmagic1 libncursesw5 libpipeline1 libpython-stdlib libpython2.7-minimal
+ bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian
+ libasprintf0v5 libcroco3 libexpat1 libffi6 libglib2.0-0 libhts1 libicu55
+ libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
- quilt sbuild-build-depends-bedtools-dummy zlib1g-dev
-0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded.
-Need to get 3682 kB/14.7 MB of archives.
-After this operation, 48.1 MB of additional disk space will be used.
-Get:1 http://ftp.jp.debian.org/debian/ unstable/main libpython2.7-minimal amd64 2.7.6-7 [347 kB]
-Get:2 http://ftp.jp.debian.org/debian/ unstable/main python2.7-minimal amd64 2.7.6-7 [1231 kB]
-Get:3 http://ftp.jp.debian.org/debian/ unstable/main libpython2.7-stdlib amd64 2.7.6-7 [1868 kB]
-Get:4 http://ftp.jp.debian.org/debian/ unstable/main python2.7 amd64 2.7.6-7 [236 kB]
+ samtools sbuild-build-depends-bedtools-dummy zlib1g-dev
+0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded.
+Need to get 621 kB/23.7 MB of archives.
+After this operation, 82.6 MB of additional disk space will be used.
+Get:1 http://ftp2.jp.debian.org/debian/ sid/main libhts1 amd64 1.2.1-1 [229 kB]
+Get:2 http://ftp2.jp.debian.org/debian/ sid/main samtools amd64 1.2-1 [392 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 3682 kB in 2s (1723 kB/s)
-Selecting previously unselected package libncursesw5:amd64.
-(Reading database ... 11224 files and directories currently installed.)
-Preparing to unpack .../libncursesw5_5.9+20140118-1_amd64.deb ...
-Unpacking libncursesw5:amd64 (5.9+20140118-1) ...
-Selecting previously unselected package libpipeline1:amd64.
-Preparing to unpack .../libpipeline1_1.2.6-2_amd64.deb ...
-Unpacking libpipeline1:amd64 (1.2.6-2) ...
-Selecting previously unselected package libssl1.0.0:amd64.
-Preparing to unpack .../libssl1.0.0_1.0.1f-1_amd64.deb ...
-Unpacking libssl1.0.0:amd64 (1.0.1f-1) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.2-5_amd64.deb ...
-Unpacking groff-base (1.22.2-5) ...
-Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ...
-Unpacking bsdmainutils (9.0.5) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.6.6-1_amd64.deb ...
-Unpacking man-db (2.6.6-1) ...
-Selecting previously unselected package libasprintf0c2:amd64.
-Preparing to unpack .../libasprintf0c2_0.18.3.2-1_amd64.deb ...
-Unpacking libasprintf0c2:amd64 (0.18.3.2-1) ...
-Selecting previously unselected package libmagic1:amd64.
-Preparing to unpack .../libmagic1_1%3a5.17-1_amd64.deb ...
-Unpacking libmagic1:amd64 (1:5.17-1) ...
-Selecting previously unselected package libsqlite3-0:amd64.
-Preparing to unpack .../libsqlite3-0_3.8.3.1-1_amd64.deb ...
-Unpacking libsqlite3-0:amd64 (3.8.3.1-1) ...
-Selecting previously unselected package libxml2:amd64.
-Preparing to unpack .../libxml2_2.9.1+dfsg1-3_amd64.deb ...
-Unpacking libxml2:amd64 (2.9.1+dfsg1-3) ...
-Selecting previously unselected package libffi6:amd64.
-Preparing to unpack .../libffi6_3.0.13-12_amd64.deb ...
-Unpacking libffi6:amd64 (3.0.13-12) ...
-Selecting previously unselected package libglib2.0-0:amd64.
-Preparing to unpack .../libglib2.0-0_2.38.2-5_amd64.deb ...
-Unpacking libglib2.0-0:amd64 (2.38.2-5) ...
-Selecting previously unselected package libcroco3:amd64.
-Preparing to unpack .../libcroco3_0.6.8-2_amd64.deb ...
-Unpacking libcroco3:amd64 (0.6.8-2) ...
-Selecting previously unselected package libexpat1:amd64.
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-Unpacking mime-support (3.54) ...
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-Unpacking libpython2.7-stdlib:amd64 (2.7.6-7) ...
-Selecting previously unselected package python2.7.
-Preparing to unpack .../python2.7_2.7.6-7_amd64.deb ...
-Unpacking python2.7 (2.7.6-7) ...
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-Unpacking python-minimal (2.7.5-5) ...
-Selecting previously unselected package libpython-stdlib:amd64.
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-Unpacking libpython-stdlib:amd64 (2.7.5-5) ...
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-Unpacking python (2.7.5-5) ...
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-Unpacking intltool-debian (0.35.0+20060710.1) ...
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-Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ...
-Selecting previously unselected package sbuild-build-depends-bedtools-dummy.
-Preparing to unpack .../sbuild-build-depends-bedtools-dummy.deb ...
-Unpacking sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
-Setting up libncursesw5:amd64 (5.9+20140118-1) ...
-Setting up libpipeline1:amd64 (1.2.6-2) ...
-Setting up libssl1.0.0:amd64 (1.0.1f-1) ...
-Setting up groff-base (1.22.2-5) ...
-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 (2.6.6-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up libasprintf0c2:amd64 (0.18.3.2-1) ...
-Setting up libmagic1:amd64 (1:5.17-1) ...
-Setting up libsqlite3-0:amd64 (3.8.3.1-1) ...
-Setting up libxml2:amd64 (2.9.1+dfsg1-3) ...
-Setting up libffi6:amd64 (3.0.13-12) ...
-Setting up libglib2.0-0:amd64 (2.38.2-5) ...
-No schema files found: doing nothing.
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-Setting up libexpat1:amd64 (2.1.0-4) ...
-Setting up libunistring0:amd64 (0.9.3-5) ...
-Setting up libpython2.7-minimal:amd64 (2.7.6-7) ...
-Setting up python2.7-minimal (2.7.6-7) ...
-Setting up file (1:5.17-1) ...
-Setting up gettext-base (0.18.3.2-1) ...
-Setting up mime-support (3.54) ...
-update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
-Setting up libpython2.7-stdlib:amd64 (2.7.6-7) ...
-Setting up python2.7 (2.7.6-7) ...
-Setting up python-minimal (2.7.5-5) ...
-Setting up libpython-stdlib:amd64 (2.7.5-5) ...
-Setting up python (2.7.5-5) ...
-Setting up cdbs (0.4.122) ...
-Setting up gettext (0.18.3.2-1) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20140228) ...
-Setting up diffstat (1.58-1) ...
-Setting up quilt (0.61-1) ...
-Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ...
-Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.18-4) ...
+Fetched 621 kB in 4s (155 kB/s)
+Selecting previously unselected package libasprintf0v5:amd64.
+(Reading database ...
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+Preparing to unpack .../libasprintf0v5_0.19.5.1-1_amd64.deb ...
+Unpacking libasprintf0v5:amd64 (0.19.5.1-1) ...
+Selecting previously unselected package libmagic1:amd64.
+Preparing to unpack .../libmagic1_1%3a5.22+15-2_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.22+15-2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_amd64.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_amd64.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:amd64.
+Preparing to unpack .../libpipeline1_1.4.1-1_amd64.deb ...
+Unpacking libpipeline1:amd64 (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.2-1_amd64.deb ...
+Unpacking man-db (2.7.2-1) ...
+Selecting previously unselected package libpython2.7-minimal:amd64.
+Preparing to unpack .../libpython2.7-minimal_2.7.10-3_amd64.deb ...
+Unpacking libpython2.7-minimal:amd64 (2.7.10-3) ...
+Selecting previously unselected package python2.7-minimal.
+Preparing to unpack .../python2.7-minimal_2.7.10-3_amd64.deb ...
+Unpacking python2.7-minimal (2.7.10-3) ...
+Selecting previously unselected package python-minimal.
+Preparing to unpack .../python-minimal_2.7.9-1_amd64.deb ...
+Unpacking python-minimal (2.7.9-1) ...
+Selecting previously unselected package mime-support.
+Preparing to unpack .../mime-support_3.59_all.deb ...
+Unpacking mime-support (3.59) ...
+Selecting previously unselected package libexpat1:amd64.
+Preparing to unpack .../libexpat1_2.1.0-7_amd64.deb ...
+Unpacking libexpat1:amd64 (2.1.0-7) ...
+Selecting previously unselected package libffi6:amd64.
+Preparing to unpack .../libffi6_3.2.1-3_amd64.deb ...
+Unpacking libffi6:amd64 (3.2.1-3) ...
+Selecting previously unselected package libsqlite3-0:amd64.
+Preparing to unpack .../libsqlite3-0_3.8.11.1-1_amd64.deb ...
+Unpacking libsqlite3-0:amd64 (3.8.11.1-1) ...
+Selecting previously unselected package libssl1.0.0:amd64.
+Preparing to unpack .../libssl1.0.0_1.0.2d-1_amd64.deb ...
+Unpacking libssl1.0.0:amd64 (1.0.2d-1) ...
+Selecting previously unselected package libpython2.7-stdlib:amd64.
+Preparing to unpack .../libpython2.7-stdlib_2.7.10-3_amd64.deb ...
+Unpacking libpython2.7-stdlib:amd64 (2.7.10-3) ...
+Selecting previously unselected package python2.7.
+Preparing to unpack .../python2.7_2.7.10-3_amd64.deb ...
+Unpacking python2.7 (2.7.10-3) ...
+Selecting previously unselected package libpython-stdlib:amd64.
+Preparing to unpack .../libpython-stdlib_2.7.9-1_amd64.deb ...
+Unpacking libpython-stdlib:amd64 (2.7.9-1) ...
+Setting up libpython2.7-minimal:amd64 (2.7.10-3) ...
+Setting up python2.7-minimal (2.7.10-3) ...
+Setting up python-minimal (2.7.9-1) ...
+Selecting previously unselected package python.
+(Reading database ...
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(Reading database ... 13245 files and directories currently installed.)
+Preparing to unpack .../python_2.7.9-1_amd64.deb ...
+Unpacking python (2.7.9-1) ...
+Selecting previously unselected package libglib2.0-0:amd64.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_amd64.deb ...
+Unpacking libglib2.0-0:amd64 (2.44.1-1.1) ...
+Selecting previously unselected package libicu55:amd64.
+Preparing to unpack .../libicu55_55.1-4_amd64.deb ...
+Unpacking libicu55:amd64 (55.1-4) ...
+Selecting previously unselected package libxml2:amd64.
+Preparing to unpack .../libxml2_2.9.2+really2.9.1+dfsg1-0.1_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.1) ...
+Selecting previously unselected package libcroco3:amd64.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ...
+Unpacking libcroco3:amd64 (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:amd64.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ...
+Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.22+15-2_amd64.deb ...
+Unpacking file (1:5.22+15-2) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.5.1-1_amd64.deb ...
+Unpacking gettext-base (0.19.5.1-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.5.1-1_amd64.deb ...
+Unpacking gettext (0.19.5.1-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.2_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.2) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:amd64.
+Preparing to unpack .../libhts1_1.2.1-1_amd64.deb ...
+Unpacking libhts1:amd64 (1.2.1-1) ...
+Selecting previously unselected package samtools.
+Preparing to unpack .../samtools_1.2-1_amd64.deb ...
+Unpacking samtools (1.2-1) ...
+Selecting previously unselected package zlib1g-dev:amd64.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Selecting previously unselected package sbuild-build-depends-bedtools-dummy.
+Preparing to unpack .../sbuild-build-depends-bedtools-dummy.deb ...
+Unpacking sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
+Setting up libasprintf0v5:amd64 (0.19.5.1-1) ...
+Setting up libmagic1:amd64 (1:5.22+15-2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+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 libpipeline1:amd64 (1.4.1-1) ...
+Setting up man-db (2.7.2-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up mime-support (3.59) ...
+Setting up libexpat1:amd64 (2.1.0-7) ...
+Setting up libffi6:amd64 (3.2.1-3) ...
+Setting up libsqlite3-0:amd64 (3.8.11.1-1) ...
+Setting up libssl1.0.0:amd64 (1.0.2d-1) ...
+Setting up libpython2.7-stdlib:amd64 (2.7.10-3) ...
+Setting up python2.7 (2.7.10-3) ...
+Setting up libpython-stdlib:amd64 (2.7.9-1) ...
+Setting up python (2.7.9-1) ...
+Setting up libglib2.0-0:amd64 (2.44.1-1.1) ...
+No schema files found: doing nothing.
+Setting up libicu55:amd64 (55.1-4) ...
+Setting up libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.1) ...
+Setting up libcroco3:amd64 (0.6.8-3+b1) ...
+Setting up libunistring0:amd64 (0.9.3-5.2+b1) ...
+Setting up file (1:5.22+15-2) ...
+Setting up gettext-base (0.19.5.1-1) ...
+Setting up gettext (0.19.5.1-1) ...
+Setting up intltool-debian (0.35.0+20060710.2) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:amd64 (1.2.1-1) ...
+Setting up samtools (1.2-1) ...
+Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-19) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.12-1-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.24-4 dpkg-dev_1.17.6 g++-4.8_4.8.2-16 gcc-4.8_4.8.2-16 libc6-dev_2.18-4 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 linux-libc-dev_3.13.6-1
-Package versions: apt_0.9.16.1 base-files_7.2 base-passwd_3.5.32 bash_4.3-3 binutils_2.24-4 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.6 build-essential_11.6 bzip2_1.0.6-5 cdbs_0.4.122 coreutils_8.21-1.1 cpp_4:4.8.2-2 cpp-4.8_4.8.2-16 dash_0.5.7-4 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20140228 debian-archive-keyring_2012.4 debianutils_4.4 diffstat_1.58-1 diffutils_1:3.3-1 dpkg_1.17.6 dpkg-dev_1.17.6 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 eatmydata_26-2 fakeroot_1.20- [...]
+Kernel: Linux 4.1.0-0.bpo.1-rt-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-5_5.2.1-16 gcc-5_5.2.1-16 libc6-dev_2.19-19 libstdc++-5-dev_5.2.1-16 libstdc++6_5.2.1-16 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.26.2-9 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-16 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 eatmydata_82- [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -273,12 +281,12 @@ Package versions: apt_0.9.16.1 base-files_7.2 base-passwd_3.5.32 bash_4.3-3 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (bedtools_2.19.1-1.dsc)
-dpkg-source: info: extracting bedtools in bedtools-2.19.1
-dpkg-source: info: unpacking bedtools_2.19.1.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.19.1-1.debian.tar.xz
+dpkg-source: warning: extracting unsigned source package (bedtools_2.25.0-1.dsc)
+dpkg-source: info: extracting bedtools in bedtools-2.25.0
+dpkg-source: info: unpacking bedtools_2.25.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.25.0-1.debian.tar.xz
dpkg-source: info: applying gzstream.h.patch
-dpkg-source: info: applying debian-changes
+dpkg-source: info: applying fix_test_script.patch
Check disc space
────────────────
@@ -289,14 +297,17 @@ User Environment
────────────────
HOME=/sbuild-nonexistent
+LD_LIBRARY_PATH=/usr/lib/libeatmydata
+LD_PRELOAD=libeatmydata.so
LOGNAME=charles
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
-SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
+PWD=/«PKGBUILDDIR»
+SCHROOT_ALIAS_NAME=unstable
+SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=unstable-amd64-sbuild-23307417-a3f6-4624-bcca-ffa4855c0f92
+SCHROOT_SESSION_ID=sid-amd64-sbuild-89a3befd-5ba5-4c3b-b1f0-5c82865b0520
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -305,37 +316,40 @@ USER=charles
USERNAME=charles
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
-XDG_SESSION_ID=6
+XDG_SESSION_ID=1
XDG_VTNR=7
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.19.1-1
+dpkg-buildpackage: source version 2.25.0-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build bedtools-2.19.1
+ dpkg-source --before-build bedtools-2.25.0
dpkg-buildpackage: host architecture amd64
-dpkg-source: info: using options from bedtools-2.19.1/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from bedtools-2.25.0/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
-test -x debian/rules
-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" 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»'
+dh clean
+ dh_testdir
+ dh_auto_clean
+ make -j1 clean
+make[1]: Entering directory '/«PKGBUILDDIR»'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-dh_clean
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
rm -rf debian/bedtools/
rm -f debian/bedtools-test.substvars
rm -f debian/bedtools-test.*.debhelper
rm -rf debian/bedtools-test/
+ rm -rf debian/.debhelper/
rm -f debian/*.debhelper.log
rm -f debian/files
- find . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -343,65 +357,22 @@ dh_clean
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
rm -f *-stamp
-/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 debian-changes
-Restoring src/utils/fileType/fileType.cpp
-Restoring src/slopBed/slopBed.h
-Restoring src/slopBed/slopBed.cpp
-Restoring test/map/test-map.sh
-Restoring test/reldist/test-reldist.sh
-Restoring test/slop/test-slop.sh
-
-Removing patch gzstream.h.patch
-Restoring src/utils/gzstream/gzstream.C
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
- dpkg-source -b bedtools-2.19.1
-dpkg-source: info: using options from bedtools-2.19.1/debian/source/options: --single-debian-patch
-dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: applying gzstream.h.patch
-dpkg-source: info: applying debian-changes
-dpkg-source: info: building bedtools using existing ./bedtools_2.19.1.orig.tar.gz
-dpkg-source: warning: file bedtools-2.19.1/test/reldist/test-reldist.sh has no final newline (either original or modified version)
-dpkg-source: warning: file bedtools-2.19.1/test/slop/test-slop.sh has no final newline (either original or modified version)
-dpkg-source: info: local changes detected, the modified files are:
- bedtools-2.19.1/src/slopBed/slopBed.cpp
- bedtools-2.19.1/src/slopBed/slopBed.h
- bedtools-2.19.1/src/utils/fileType/fileType.cpp
- bedtools-2.19.1/test/map/test-map.sh
- bedtools-2.19.1/test/reldist/test-reldist.sh
- bedtools-2.19.1/test/slop/test-slop.sh
-dpkg-source: info: local changes have been recorded in a new patch: bedtools-2.19.1/debian/patches/debian-changes
-dpkg-source: info: building bedtools in bedtools_2.19.1-1.debian.tar.xz
-dpkg-source: info: building bedtools in bedtools_2.19.1-1.dsc
+ dpkg-source -b bedtools-2.25.0
+dpkg-source: info: using options from bedtools-2.25.0/debian/source/options: --single-debian-patch
+dpkg-source: info: using source format '3.0 (quilt)'
+dpkg-source: info: building bedtools using existing ./bedtools_2.25.0.orig.tar.gz
+dpkg-source: info: building bedtools in bedtools_2.25.0-1.debian.tar.xz
+dpkg-source: info: building bedtools in bedtools_2.25.0-1.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/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 debian-changes
-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" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
-make[1]: Entering directory `/«PKGBUILDDIR»'
+dh build
+ dh_testdir
+ dh_auto_configure
+ dh_auto_build
+ make -j1
+make[1]: Entering directory '/«PKGBUILDDIR»'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.19.1
+DETECTED_VERSION = v2.25.0
CURRENT_VERSION =
Updating version file.
* Creating BamTools API
@@ -418,39 +389,65 @@ Updating version file.
- Building in src/utils/Contexts
* compiling ContextBase.cpp
* compiling ContextIntersect.cpp
+ * compiling ContextFisher.cpp
* compiling ContextMap.cpp
* compiling ContextSample.cpp
+ * compiling ContextSpacing.cpp
+ * compiling ContextMerge.cpp
+ * compiling ContextJaccard.cpp
+ * compiling ContextClosest.cpp
+ * compiling ContextSubtract.cpp
+ * compiling ContextCoverage.cpp
+ * compiling ContextComplement.cpp
+ * compiling ContextGroupBy.cpp
- Building in src/utils/FileRecordTools
+ * compiling FileRecordMgr.cpp
+ * compiling FileRecordMergeMgr.cpp
- Building in FileReaders
* compiling FileReader.cpp
- * compiling SingleLineDelimTransferBuffer.cpp
* compiling SingleLineDelimTextFileReader.cpp
* compiling BamFileReader.cpp
* compiling BufferedStreamMgr.cpp
* compiling InputStreamMgr.cpp
- Building in Records
- * compiling RecordMgr.cpp
* compiling Record.cpp
+ * compiling EmptyRecord.cpp
* compiling Bed3Interval.cpp
* compiling Bed4Interval.cpp
* compiling BedGraphInterval.cpp
* compiling Bed5Interval.cpp
* compiling Bed6Interval.cpp
+ * compiling PlusFields.cpp
* compiling BedPlusInterval.cpp
* compiling Bed12Interval.cpp
* compiling BamRecord.cpp
- * compiling VcfRecord.cpp
* compiling GffRecord.cpp
- * compiling RecordKeyList.cpp
+ * compiling GffPlusRecord.cpp
+ * compiling VcfRecord.cpp
+ * compiling NoPosPlusRecord.cpp
* compiling BlockMgr.cpp
- * compiling FileRecordMgr.cpp
+ * compiling StrandQueue.cpp
+ * compiling RecordMgr.cpp
+ * compiling RecordList.cpp
+ * compiling RecordKeyList.cpp
+ * compiling RecordKeyVector.cpp
+- Building in src/utils/FileRecordTools/FileReaders
+make[2]: Nothing to be done for 'all'.
+- Building in src/utils/FileRecordTools/Records
+make[2]: Nothing to be done for 'all'.
- Building in src/utils/general
* compiling QuickString.cpp
* compiling ParseTools.cpp
+ParseTools.cpp: In function 'int str2chrPos(const char*, size_t)':
+ParseTools.cpp:31:7: warning: unused variable 'hasExponent' [-Wunused-variable]
+ bool hasExponent = false;
+ ^
* compiling PushBackStreamBuf.cpp
* compiling CompressionTools.cpp
+ * compiling Tokenizer.cpp
+ * compiling CommonHelp.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/ [...]
- Building in src/utils/fileType
* compiling fileType.cpp
* compiling FileRecordTypeChecker.cpp
@@ -461,6 +458,7 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
* compiling KeyListOpsMethods.cpp
- Building in src/utils/NewChromsweep
* compiling NewChromsweep.cpp
+ * compiling CloseSweep.cpp
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
- Building in src/utils/tabFile
@@ -485,18 +483,18 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
* compiling BamIndexFactory_p.cpp
* compiling BamStandardIndex_p.cpp
src/api/internal/index/BamStandardIndex_p.cpp: In member function 'void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)':
-src/api/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
- ^
+ ^
* compiling BamToolsIndex_p.cpp
* compiling BamDeviceFactory_p.cpp
* compiling BamFile_p.cpp
* compiling BamFtp_p.cpp
* compiling BamHttp_p.cpp
src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendRequest(size_t)':
-src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+src/api/internal/io/BamHttp_p.cpp:396:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize );
- ^
+ ^
* compiling BamPipe_p.cpp
* compiling BgzfStream_p.cpp
* compiling ByteArray_p.cpp
@@ -522,16 +520,14 @@ ranlib lib/libbamtools.a
* compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:29:12: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- length = NULL;
- ^
-Fasta.cpp:32:15: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- line_blen = NULL;
- ^
-Fasta.cpp:33:15: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- line_len = NULL;
- ^
+Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)':
+Fasta.cpp:290:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+ fread(seq, sizeof(char), seqlen, file);
+ ^
+Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)':
+Fasta.cpp:332:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+ fread(seq, sizeof(char), (off_t) seqlen, file);
+ ^
* compiling split.cpp
- Building in src/utils/VectorOps
* compiling VectorOps.cpp
@@ -544,6 +540,10 @@ GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-
* compiling NewGenomeFile.cpp
- Building in src/utils/RecordOutputMgr
* compiling RecordOutputMgr.cpp
+- Building in src/utils/ToolBase
+ * compiling ToolBase.cpp
+- Building in src/utils/driver
+ * compiling BedtoolsDriver.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
@@ -580,9 +580,9 @@ bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused
* compiling bedToIgv.cpp
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-- Building in src/closestBed
- * compiling closestMain.cpp
- * compiling closestBed.cpp
+- Building in src/closestFile
+ * compiling closestHelp.cpp
+ * compiling closestFile.cpp
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
@@ -590,12 +590,12 @@ clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wu
bool haveMaxDistance = false;
^
* compiling clusterBed.cpp
-- Building in src/complementBed
- * compiling complementMain.cpp
- * compiling complementBed.cpp
-- Building in src/coverageBed
- * compiling coverageMain.cpp
- * compiling coverageBed.cpp
+- Building in src/complementFile
+ * compiling complementHelp.cpp
+ * compiling complementFile.cpp
+- Building in src/coverageFile
+ * compiling coverageHelp.cpp
+ * compiling coverageFile.cpp
- Building in src/expand
* compiling expand.cpp
- Building in src/fastaFromBed
@@ -615,15 +615,16 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
^
- Building in src/groupBy
* compiling groupBy.cpp
-groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- bool haveOps = true;
- ^
+ * compiling groupByHelp.cpp
- Building in src/intersectFile
- * compiling intersectMain.cpp
+ * compiling intersectHelp.cpp
* compiling intersectFile.cpp
+- Building in src/fisher
+ * compiling fisherHelp.cpp
+ * compiling fisher.cpp
+ * compiling kfunc.cpp
- Building in src/jaccard
- * compiling jaccardMain.cpp
... 3967 lines suppressed ...
--
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