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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Changed-By: Charles Plessy <[email protected]> -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: - 01cd626e00c32c4f2ca621fa928a066c8e761fc2 2027 bedtools_2.19.1-1.dsc - 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: - 68919af16fdfd584df6bcb66580ce2cb7c52754990d6266eeecd14b9029f84c9 2027 bedtools_2.19.1-1.dsc - 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' 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+phzaOKFEngqNg1sgQ/9lPRNkirZ+GOa5nBqUp1ztcfZa03V+YzFd6FTcHq+8Fnqi +Z4zbFIQQ7qhE99Gk9F7+ +=9Cpb -----END PGP SIGNATURE----- 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. -Preparing to unpack .../libexpat1_2.1.0-4_amd64.deb ... -Unpacking libexpat1:amd64 (2.1.0-4) ... -Selecting previously unselected package libunistring0:amd64. -Preparing to unpack .../libunistring0_0.9.3-5_amd64.deb ... -Unpacking libunistring0:amd64 (0.9.3-5) ... -Selecting previously unselected package libpython2.7-minimal:amd64. -Preparing to unpack .../libpython2.7-minimal_2.7.6-7_amd64.deb ... -Unpacking libpython2.7-minimal:amd64 (2.7.6-7) ... -Selecting previously unselected package python2.7-minimal. -Preparing to unpack .../python2.7-minimal_2.7.6-7_amd64.deb ... -Unpacking python2.7-minimal (2.7.6-7) ... -Selecting previously unselected package file. -Preparing to unpack .../file_1%3a5.17-1_amd64.deb ... -Unpacking file (1:5.17-1) ... -Selecting previously unselected package gettext-base. -Preparing to unpack .../gettext-base_0.18.3.2-1_amd64.deb ... -Unpacking gettext-base (0.18.3.2-1) ... -Selecting previously unselected package mime-support. -Preparing to unpack .../mime-support_3.54_all.deb ... -Unpacking mime-support (3.54) ... -Selecting previously unselected package libpython2.7-stdlib:amd64. -Preparing to unpack .../libpython2.7-stdlib_2.7.6-7_amd64.deb ... -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) ... -Selecting previously unselected package python-minimal. -Preparing to unpack .../python-minimal_2.7.5-5_amd64.deb ... -Unpacking python-minimal (2.7.5-5) ... -Selecting previously unselected package libpython-stdlib:amd64. 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(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 ... (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 .../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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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 <[email protected]> - 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 ... -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
