[med-svn] [bedtools] 01/01: bedtools (2.19.0-1) unstable; urgency=low
Charles Plessy
plessy at moszumanska.debian.org
Sun Feb 16 07:21:58 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch meta
in repository bedtools.
commit 1431d44d1a5e668abd8df8b0b96ac400b1bd2053
Author: Charles Plessy <plessy at debian.org>
Date: Sun Feb 16 16:19:25 2014 +0900
bedtools (2.19.0-1) unstable; urgency=low
e07e70c Imported Upstream version 2.19.0
afdc61a Watch GitHub at https://github.com/arq5x/bedtools2.
4abe14e Source control file normalised with config-model-edit.
0518353 Corrected a typo in the long description. (Closes: #714873)
f63d85e Follow the layout of the upstream repository.
c25f9e5 Correct name of README file in debian/docs.
5561c7c Emulate source format 1.0 in the format 3.0 (quilt).
a45a0ab Canonical VCS URLs.
4459dfe Conforms with Policy 3.9.5.
-- Charles Plessy <plessy at debian.org> Sat, 15 Feb 2014 19:39:23 +0900
---
amd64.changes | 78 ++--
amd64.log | 1385 +++++++++++++++++++++++++++++++++++++++------------------
dsc | 50 +--
upload | 12 +-
4 files changed, 1012 insertions(+), 513 deletions(-)
diff --git a/amd64.changes b/amd64.changes
index 1668cac..c299141 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -1,59 +1,61 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
Format: 1.8
-Date: Sun, 04 Nov 2012 17:59:41 +0900
+Date: Sat, 15 Feb 2014 19:39:23 +0900
Source: bedtools
Binary: bedtools
Architecture: source amd64
-Version: 2.17.0-1
+Version: 2.19.0-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
+Closes: 714873
Changes:
- bedtools (2.17.0-1) unstable; urgency=low
+ bedtools (2.19.0-1) unstable; urgency=low
.
- bb9012e Imported Upstream version 2.16.2.
- 9006b23 Imported Upstream version 2.17.0.
- 9112569 Documented BEDTools license as a whole.
- 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
- a781b14 Conforms with Policy 3.9.4.
- 84b1167 Use Debhelper 9.
- 0bf572d Distribute the test suite.
- 422cd34 Bash completion for BEDTools.
+ e07e70c Imported Upstream version 2.19.0
+ afdc61a Watch GitHub at https://github.com/arq5x/bedtools2.
+ 4abe14e Source control file normalised with config-model-edit.
+ 0518353 Corrected a typo in the long description. (Closes: #714873)
+ f63d85e Follow the layout of the upstream repository.
+ c25f9e5 Correct name of README file in debian/docs.
+ 5561c7c Emulate source format 1.0 in the format 3.0 (quilt).
+ a45a0ab Canonical VCS URLs.
+ 4459dfe Conforms with Policy 3.9.5.
Checksums-Sha1:
- d07a43dc729f8a32adb2fab0520bea939d03b7cb 1951 bedtools_2.17.0-1.dsc
- 1b1de3c35394a423f9ad98a9957a8853b426a578 1208640 bedtools_2.17.0.orig.tar.gz
- 178f43b7d30d964f35d60461ec2859eabce93471 5663 bedtools_2.17.0-1.debian.tar.gz
- 212e9c037b2566c6594b2eaf64f6cbbf1239f587 442978 bedtools_2.17.0-1_amd64.deb
+ befe8cf1409e05cdb4e020320191f948011cd996 1949 bedtools_2.19.0-1.dsc
+ 1ed6b86fd8c9867b187b3024dc3b68603f935dbb 4117988 bedtools_2.19.0.orig.tar.gz
+ 6809986218ee54154a525d64f361d9c0430b16fc 6860 bedtools_2.19.0-1.debian.tar.xz
+ bc3aad74cf182a537cc606f509631c894c91c86f 554664 bedtools_2.19.0-1_amd64.deb
Checksums-Sha256:
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- 6dcfacdcbccc968e872b81ba1f37a086b1bcc486571582ed595db717e924d0fe 1208640 bedtools_2.17.0.orig.tar.gz
- 82ee0bb3cb16bd8a9dc4e273641b31524a98ef798289b1fac13297b5ef6b4c94 5663 bedtools_2.17.0-1.debian.tar.gz
- 4827f2b603828fe4c208338e5ede1cd3c1558cc44cd598a75c4944e5aa6f0e54 442978 bedtools_2.17.0-1_amd64.deb
+ addba2a7f0d2c5c5f0ba08702dfdc002ca49553e601c72836db9897eb384aa4a 1949 bedtools_2.19.0-1.dsc
+ 79294fc5998df941f0494819be74c0d64836404def51b5b5d52a4c2d2775cbbf 4117988 bedtools_2.19.0.orig.tar.gz
+ 30b201f18e8b9b2fe3d9b7f754c09f78ef6365059e4f49e5697c3cd882e73f4f 6860 bedtools_2.19.0-1.debian.tar.xz
+ 704791408946067d329acdd690b8fa9fb3ea33c9615648121f1a57e434c5a8fd 554664 bedtools_2.19.0-1_amd64.deb
Files:
- ccf2adde8093af86c778a019e2030b5e 1951 science optional bedtools_2.17.0-1.dsc
- e7209a6f88f8df844474369bd40db8be 1208640 science optional bedtools_2.17.0.orig.tar.gz
- b99bb92be5d8b0fa086b3649ca4ab2e0 5663 science optional bedtools_2.17.0-1.debian.tar.gz
- 49782533b9a654663db3b8cad52954f6 442978 science optional bedtools_2.17.0-1_amd64.deb
+ 7fff6e3ef7e6e14757fc63d2501b0a7b 1949 science optional bedtools_2.19.0-1.dsc
+ 3faf6450d9b0e82f42347d00da2c6083 4117988 science optional bedtools_2.19.0.orig.tar.gz
+ 709fd7028e719c53479b630bcbb4f0e0 6860 science optional bedtools_2.19.0-1.debian.tar.xz
+ b844b6f14b50dd45c39b48ae7e593da8 554664 science optional bedtools_2.19.0-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index f462d5f..4b5dfc7 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,29 +1,29 @@
-sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on aqwa.igloo
+sbuild (Debian sbuild) 0.64.1 (13 Oct 2013) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.17.0-1 (amd64) 04 nov. 2012 18:00 ║
+║ bedtools 2.19.0-1 (amd64) 16 févr. 2014 16:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.17.0-1
-Source Version: 2.17.0-1
+Version: 2.19.0-1
+Source Version: 2.19.0-1
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/bedtools-BUAVVH/bedtools-2.17.0' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/bedtools-BUAVVH' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-ece15667-d6d5-42aa-899b-e50347c7dc26' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/bedtools-TQpP0Y/bedtools-2.19.0' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bedtools-TQpP0Y' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-e234c872-e182-4ec7-b436-c6d4be4bfea2' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Hit ftp://ftp.jp.debian.org sid InRelease
-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
+Hit http://ftp.jp.debian.org unstable/main Sources/DiffIndex
+Hit http://ftp.jp.debian.org unstable/main amd64 Packages/DiffIndex
+Hit http://ftp.jp.debian.org unstable/main Translation-en/DiffIndex
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -38,14 +38,14 @@ Reading state information...
Local sources
─────────────
-bedtools_2.17.0-1.dsc exists in .; copying to chroot
+bedtools_2.19.0-1.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-cetBCc/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-1qQ4Yi/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -61,15 +61,16 @@ 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/716 B of archives.
+Need to get 0 B/822 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 10943 files and directories currently installed.)
-Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
+(Reading database ... 11208 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, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
-Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, 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-2Mk39o/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
+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-APjFJ2/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
OK
Reading package lists...
@@ -83,171 +84,184 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
- libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
- libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
- po-debconf python python-minimal python2.7 python2.7-minimal quilt
- zlib1g-dev
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libglib2.0-0
+ libmagic1 libncursesw5 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
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
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
+ libglib2.0-data shared-mime-info libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
- libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
- 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
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libglib2.0-0
+ libmagic1 libncursesw5 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 15.9 MB/17.1 MB of archives.
-After this operation, 47.2 MB of additional disk space will be used.
-Get:1 ftp://ftp.jp.debian.org/debian/ sid/main libpipeline1 amd64 1.2.2-1 [39.9 kB]
-Get:2 ftp://ftp.jp.debian.org/debian/ sid/main libssl1.0.0 amd64 1.0.1c-4 [1213 kB]
-Get:3 ftp://ftp.jp.debian.org/debian/ sid/main libmagic1 amd64 5.11-2 [202 kB]
-Get:4 ftp://ftp.jp.debian.org/debian/ sid/main libpcre3 amd64 1:8.31-1 [247 kB]
-Get:5 ftp://ftp.jp.debian.org/debian/ sid/main libsqlite3-0 amd64 3.7.14.1-1 [457 kB]
-Get:6 ftp://ftp.jp.debian.org/debian/ sid/main libxml2 amd64 2.8.0+dfsg1-6 [903 kB]
-Get:7 ftp://ftp.jp.debian.org/debian/ sid/main libglib2.0-0 amd64 2.33.12+really2.32.4-3 [1838 kB]
-Get:8 ftp://ftp.jp.debian.org/debian/ sid/main libcroco3 amd64 0.6.6-1 [134 kB]
-Get:9 ftp://ftp.jp.debian.org/debian/ sid/main libexpat1 amd64 2.1.0-1 [141 kB]
-Get:10 ftp://ftp.jp.debian.org/debian/ sid/main libgettextpo0 amd64 0.18.1.1-9 [145 kB]
-Get:11 ftp://ftp.jp.debian.org/debian/ sid/main bsdmainutils amd64 9.0.3 [209 kB]
-Get:12 ftp://ftp.jp.debian.org/debian/ sid/main groff-base amd64 1.21-9 [1153 kB]
-Get:13 ftp://ftp.jp.debian.org/debian/ sid/main man-db amd64 2.6.3-1 [1062 kB]
-Get:14 ftp://ftp.jp.debian.org/debian/ sid/main file amd64 5.11-2 [51.8 kB]
-Get:15 ftp://ftp.jp.debian.org/debian/ sid/main mime-support all 3.52-2 [35.2 kB]
-Get:16 ftp://ftp.jp.debian.org/debian/ sid/main python2.7-minimal amd64 2.7.3-5 [1761 kB]
-Get:17 ftp://ftp.jp.debian.org/debian/ sid/main python2.7 amd64 2.7.3-5 [2749 kB]
-Get:18 ftp://ftp.jp.debian.org/debian/ sid/main python-minimal all 2.7.3-3 [42.5 kB]
-Get:19 ftp://ftp.jp.debian.org/debian/ sid/main python all 2.7.3-3 [179 kB]
-Get:20 ftp://ftp.jp.debian.org/debian/ sid/main cdbs all 0.4.118 [80.0 kB]
-Get:21 ftp://ftp.jp.debian.org/debian/ sid/main gettext amd64 0.18.1.1-9 [1975 kB]
-Get:22 ftp://ftp.jp.debian.org/debian/ sid/main debhelper all 9.20120909 [705 kB]
-Get:23 ftp://ftp.jp.debian.org/debian/ sid/main diffstat amd64 1.55-3 [30.0 kB]
-Get:24 ftp://ftp.jp.debian.org/debian/ sid/main quilt all 0.60-2 [377 kB]
-Get:25 ftp://ftp.jp.debian.org/debian/ sid/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB]
+Need to get 2662 kB/14.7 MB of archives.
+After this operation, 47.9 MB of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main libpipeline1 amd64 1.2.6-2 [25.1 kB]
+Get:2 http://ftp.jp.debian.org/debian/ unstable/main libsqlite3-0 amd64 3.8.3.1-1 [406 kB]
+Get:3 http://ftp.jp.debian.org/debian/ unstable/main libglib2.0-0 amd64 2.38.2-5 [2231 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 15.9 MB in 16s (987 kB/s)
+Fetched 2662 kB in 3s (736 kB/s)
Selecting previously unselected package libncursesw5:amd64.
-(Reading database ... 10943 files and directories currently installed.)
-Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9-10_amd64.deb) ...
+(Reading database ... 11208 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.
-Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-1_amd64.deb) ...
+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.
-Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1c-4_amd64.deb) ...
+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.
-Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-9_amd64.deb) ...
+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.
-Unpacking libmagic1:amd64 (from .../libmagic1_5.11-2_amd64.deb) ...
-Selecting previously unselected package libpcre3:amd64.
-Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.31-1_amd64.deb) ...
+Preparing to unpack .../libmagic1_1%3a5.14-2_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.14-2) ...
Selecting previously unselected package libsqlite3-0:amd64.
-Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.14.1-1_amd64.deb) ...
+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.
-Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-6_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+dfsg1-3_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.
-Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-3_amd64.deb) ...
+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.
-Unpacking libcroco3:amd64 (from .../libcroco3_0.6.6-1_amd64.deb) ...
+Preparing to unpack .../libcroco3_0.6.8-2_amd64.deb ...
+Unpacking libcroco3:amd64 (0.6.8-2) ...
Selecting previously unselected package libexpat1:amd64.
-Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-1_amd64.deb) ...
+Preparing to unpack .../libexpat1_2.1.0-4_amd64.deb ...
+Unpacking libexpat1:amd64 (2.1.0-4) ...
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_0.18.1.1-9_amd64.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_amd64.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_amd64.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-1_amd64.deb) ...
+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_2.7.6-5_amd64.deb ...
+Unpacking libpython2.7-minimal:amd64 (2.7.6-5) ...
+Selecting previously unselected package python2.7-minimal.
+Preparing to unpack .../python2.7-minimal_2.7.6-5_amd64.deb ...
+Unpacking python2.7-minimal (2.7.6-5) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_amd64.deb) ...
+Preparing to unpack .../file_1%3a5.14-2_amd64.deb ...
+Unpacking file (1:5.14-2) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_amd64.deb) ...
+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.
-Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
-Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_amd64.deb) ...
+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_2.7.6-5_amd64.deb ...
+Unpacking libpython2.7-stdlib:amd64 (2.7.6-5) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3-5_amd64.deb) ...
+Preparing to unpack .../python2.7_2.7.6-5_amd64.deb ...
+Unpacking python2.7 (2.7.6-5) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
+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.
+Preparing to unpack .../libpython-stdlib_2.7.5-5_amd64.deb ...
+Unpacking libpython-stdlib:amd64 (2.7.5-5) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.3-3_all.deb) ...
+Preparing to unpack .../python_2.7.5-5_amd64.deb ...
+Unpacking python (2.7.5-5) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
+Preparing to unpack .../archives/cdbs_0.4.122_all.deb ...
+Unpacking cdbs (0.4.122) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_amd64.deb) ...
+Preparing to unpack .../gettext_0.18.3.2-1_amd64.deb ...
+Unpacking gettext (0.18.3.2-1) ...
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+nmu2_all.deb ...
+Unpacking po-debconf (1.0.16+nmu2) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
+Preparing to unpack .../debhelper_9.20131227_all.deb ...
+Unpacking debhelper (9.20131227) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_amd64.deb) ...
+Preparing to unpack .../diffstat_1.58-1_amd64.deb ...
+Unpacking diffstat (1.58-1) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Preparing to unpack .../archives/quilt_0.61-1_all.deb ...
+Unpacking quilt (0.61-1) ...
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-1_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-bedtools-dummy.
-Unpacking sbuild-build-depends-bedtools-dummy (from .../sbuild-build-depends-bedtools-dummy.deb) ...
-Setting up libncursesw5:amd64 (5.9-10) ...
-Setting up libpipeline1:amd64 (1.2.2-1) ...
-Setting up libssl1.0.0:amd64 (1.0.1c-4) ...
-Setting up libasprintf0c2:amd64 (0.18.1.1-9) ...
-Setting up libmagic1:amd64 (5.11-2) ...
-Setting up libpcre3:amd64 (1:8.31-1) ...
-Setting up libsqlite3-0:amd64 (3.7.14.1-1) ...
-Setting up libxml2:amd64 (2.8.0+dfsg1-6) ...
-Setting up libffi5:amd64 (3.0.10-3) ...
-Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-3) ...
-No schema files found: doing nothing.
-Setting up libcroco3:amd64 (0.6.6-1) ...
-Setting up libexpat1:amd64 (2.1.0-1) ...
-Setting up libunistring0:amd64 (0.9.3-5) ...
-Setting up libgettextpo0:amd64 (0.18.1.1-9) ...
-Setting up bsdmainutils (9.0.3) ...
+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 groff-base (1.21-9) ...
-Setting up man-db (2.6.3-1) ...
-Building database of manual pages ...
-Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up mime-support (3.52-2) ...
+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 (1:5.14-2) ...
+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.
+Setting up libcroco3:amd64 (0.6.8-2) ...
+Setting up libexpat1:amd64 (2.1.0-4) ...
+Setting up libunistring0:amd64 (0.9.3-5) ...
+Setting up libpython2.7-minimal:amd64 (2.7.6-5) ...
+Setting up python2.7-minimal (2.7.6-5) ...
+Setting up file (1:5.14-2) ...
+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 python2.7-minimal (2.7.3-5) ...
-Setting up python2.7 (2.7.3-5) ...
-Setting up python-minimal (2.7.3-3) ...
-Setting up python (2.7.3-3) ...
-Setting up cdbs (0.4.118) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libpython2.7-stdlib:amd64 (2.7.6-5) ...
+Setting up python2.7 (2.7.6-5) ...
+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 (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ...
+Setting up debhelper (9.20131227) ...
+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 (2.17-97) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.2.0-3-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 linux-libc-dev_3.2.32-1
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.1 [...]
+Kernel: Linux 3.12-1-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.24-3 dpkg-dev_1.17.6 g++-4.8_4.8.2-15 gcc-4.8_4.8.2-15 libc6-dev_2.17-97 libstdc++-4.8-dev_4.8.2-15 libstdc++6_4.8.2-15 linux-libc-dev_3.12.9-1
+Package versions: apt_0.9.15.2 base-files_7.2 base-passwd_3.5.32 bash_4.2+dfsg-1 binutils_2.24-3 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 cpp_4:4.8.2-2 cpp-4.8_4.8.2-15 dash_0.5.7-4 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20131227 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. [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -257,11 +271,12 @@ Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (bedtools_2.17.0-1.dsc)
-dpkg-source: info: extracting bedtools in bedtools-2.17.0
-dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
+dpkg-source: warning: extracting unsigned source package (bedtools_2.19.0-1.dsc)
+dpkg-source: info: extracting bedtools in bedtools-2.19.0
+dpkg-source: info: unpacking bedtools_2.19.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.19.0-1.debian.tar.xz
dpkg-source: info: applying gzstream.h.patch
+dpkg-source: info: applying debian-changes
Check disc space
────────────────
@@ -274,30 +289,35 @@ 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=chroot:sid-amd64-sbuild
-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-ece15667-d6d5-42aa-899b-e50347c7dc26
+SCHROOT_SESSION_ID=unstable-amd64-sbuild-e234c872-e182-4ec7-b436-c6d4be4bfea2
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
TERM=xterm
USER=charles
USERNAME=charles
+XDG_RUNTIME_DIR=/run/user/1000
+XDG_SEAT=seat0
+XDG_SESSION_ID=2
+XDG_VTNR=7
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.17.0-1
+dpkg-buildpackage: source version 2.19.0-1
+dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build bedtools-2.17.0
+ dpkg-source --before-build bedtools-2.19.0
dpkg-buildpackage: host architecture amd64
+dpkg-source: info: using options from bedtools-2.19.0/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" 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»'
@@ -315,8 +335,8 @@ dh_clean
-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 \
- \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ \) -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»'
@@ -325,18 +345,31 @@ 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 docs/content/related-tools.rst
+Restoring docs/content/installation.rst
+Restoring README.md
+
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-2.17.0
+ dpkg-source -b bedtools-2.19.0
+dpkg-source: info: using options from bedtools-2.19.0/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: building bedtools using existing ./bedtools_2.17.0.orig.tar.gz
-dpkg-source: info: building bedtools in bedtools_2.17.0-1.debian.tar.gz
-dpkg-source: info: building bedtools in bedtools_2.17.0-1.dsc
+dpkg-source: info: applying debian-changes
+dpkg-source: info: building bedtools using existing ./bedtools_2.19.0.orig.tar.gz
+dpkg-source: warning: file bedtools-2.19.0/docs/content/related-tools.rst has no final newline (either original or modified version)
+dpkg-source: info: local changes detected, the modified files are:
+ bedtools-2.19.0/README.md
+ bedtools-2.19.0/docs/content/installation.rst
+ bedtools-2.19.0/docs/content/related-tools.rst
+dpkg-source: info: local changes have been recorded in a new patch: bedtools-2.19.0/debian/patches/debian-changes
+dpkg-source: info: building bedtools in bedtools_2.19.0-1.debian.tar.xz
+dpkg-source: info: building bedtools in bedtools_2.19.0-1.dsc
debian/rules build
test -x debian/rules
mkdir -p "."
@@ -347,7 +380,7 @@ 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 gzstream.h.patch
+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»'
@@ -357,24 +390,63 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Entering directory `/«PKGBUILDDIR»'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.17.0
+DETECTED_VERSION = v2.19.0
CURRENT_VERSION =
Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
+- Building in src/utils/BinTree
+ * compiling BinTree.cpp
- Building in src/utils/version
* compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
+- Building in src/utils/Contexts
+ * compiling ContextBase.cpp
+ * compiling ContextIntersect.cpp
+ * compiling ContextMap.cpp
+ * compiling ContextSample.cpp
+- Building in src/utils/FileRecordTools
+- 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 Bed3Interval.cpp
+ * compiling Bed4Interval.cpp
+ * compiling BedGraphInterval.cpp
+ * compiling Bed5Interval.cpp
+ * compiling Bed6Interval.cpp
+ * compiling BedPlusInterval.cpp
+ * compiling Bed12Interval.cpp
+ * compiling BamRecord.cpp
+ * compiling VcfRecord.cpp
+ * compiling GffRecord.cpp
+ * compiling RecordKeyList.cpp
+ * compiling BlockMgr.cpp
+ * compiling FileRecordMgr.cpp
+- Building in src/utils/general
+ * compiling QuickString.cpp
+ * compiling ParseTools.cpp
+ * compiling PushBackStreamBuf.cpp
+ * compiling CompressionTools.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.
- Building in src/utils/fileType
* compiling fileType.cpp
+ * compiling FileRecordTypeChecker.cpp
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
+- Building in src/utils/NewChromsweep
+ * compiling NewChromsweep.cpp
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
- Building in src/utils/tabFile
@@ -400,6 +472,8 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
* 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]
+ if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
+ ^
* compiling BamToolsIndex_p.cpp
* compiling BamDeviceFactory_p.cpp
* compiling BamFile_p.cpp
@@ -407,6 +481,8 @@ src/api/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison betwee
* 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]
+ return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize );
+ ^
* compiling BamPipe_p.cpp
* compiling BgzfStream_p.cpp
* compiling ByteArray_p.cpp
@@ -418,8 +494,6 @@ src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and
* compiling TcpSocketEngine_p.cpp
* compiling TcpSocketEngine_unix_p.cpp
* compiling TcpSocket_p.cpp
-src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
-src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
* compiling SamFormatParser_p.cpp
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
@@ -432,48 +506,62 @@ ranlib lib/libbamtools.a
* compiling BamAncillary.cpp
- Building in src/utils/BlockedIntervals
* compiling BlockedIntervals.cpp
- * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
+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;
+ ^
* compiling split.cpp
- Building in src/utils/VectorOps
* compiling VectorOps.cpp
-- Building in src/utils/genomeFile
- * compiling genomeFile.cpp
-genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
-genomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
+- Building in src/utils/GenomeFile
+ * compiling GenomeFile.cpp
+GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
+GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
+ long c2;
+ ^
+ * compiling NewGenomeFile.cpp
+- Building in src/utils/RecordOutputMgr
+ * compiling RecordOutputMgr.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+ bool haveTitles = false;
+ ^
* compiling annotateBed.cpp
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
-bamToBed.cpp:85:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
+bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
+ bool useAlignmentScore = false;
+ ^
- Building in src/bamToFastq
* compiling bamToFastqMain.cpp
bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ bool haveFastq2 = false;
+ ^
* compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+ bool haveMapQual = false;
+ ^
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+ bool haveMapQual = false;
+ ^
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- Building in src/bed12ToBed6
@@ -485,6 +573,8 @@ bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ bool haveMaxDistance = false;
+ ^
* compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
@@ -507,13 +597,17 @@ clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wu
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+ bool haveColumns = false;
+ ^
- 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]
-- Building in src/intersectBed
+ bool haveOps = true;
+ ^
+- Building in src/intersectFile
* compiling intersectMain.cpp
- * compiling intersectBed.cpp
+ * compiling intersectFile.cpp
- Building in src/jaccard
* compiling jaccardMain.cpp
* compiling jaccard.cpp
@@ -523,31 +617,44 @@ groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-se
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-- Building in src/mapBed
+- Building in src/mapFile
* compiling mapMain.cpp
-mapMain.cpp: In function 'int map_main(int, char**)':
-mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
-mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
- * compiling mapBed.cpp
+ * compiling mapFile.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ bool haveMaxDistance = false;
+ ^
* compiling mergeBed.cpp
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+ bool haveBed = false;
+ ^
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ bool haveBams = false;
+ ^
multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ bool haveFraction = false;
+ ^
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+ bool haveFiles = false;
+ ^
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+ bool haveGenome = false;
+ ^
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ bool haveFiller = true;
+ ^
* compiling multiIntersectBed.cpp
+- Building in src/nekSandbox1
+ * compiling nekSandboxMain.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
@@ -555,22 +662,43 @@ multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ bool haveFraction = false;
+ ^
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+ CHRPOS spanLength = 0;
+ ^
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+ int spanLength = 0;
+ ^
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ bool haveFraction = false;
+ ^
* compiling pairToPair.cpp
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
+ bool found1 = false;
+ ^
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
+ bool found2 = false;
+ ^
- Building in src/randomBed
* compiling randomBedMain.cpp
* compiling randomBed.cpp
+- Building in src/regressTest
+compiling RegressTest.cpp
+compiling regressTestMain.cpp
+- Building in src/reldist
+ * compiling reldistMain.cpp
+ * compiling reldist.cpp
+- Building in src/sampleFile
+ * compiling sampleMain.cpp
+ * compiling SampleFile.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
@@ -582,20 +710,26 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
* compiling sortBed.cpp
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int subtract_main(int, char**)':
-subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ bool haveFraction = false;
+ ^
* compiling tagBam.cpp
- Building in src/unionBedGraphs
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+ bool haveFiles = false;
+ ^
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+ bool haveGenome = false;
+ ^
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ bool haveFiller = true;
+ ^
* compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
@@ -628,7 +762,7 @@ Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
- cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ cp -a README.md debian/bedtools/usr/share/doc/bedtools
chown -R 0:0 debian/bedtools/usr/share/doc
chmod -R go=rX debian/bedtools/usr/share/doc
chmod -R u\+rw debian/bedtools/usr/share/doc
@@ -712,6 +846,8 @@ dh_install -pbedtools
cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/reldist debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/sample debian/bedtools/usr/share/bedtools/test/
cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
@@ -724,8 +860,8 @@ dh_strip -pbedtools
strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools -X test
cd debian/bedtools
- chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
- gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
cd '/«PKGBUILDDIR»'
dh_fixperms -pbedtools
find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -753,6 +889,7 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
echo misc:Depends= >> debian/bedtools.substvars
dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 644 debian/bedtools/DEBIAN/control
chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
@@ -761,14 +898,16 @@ dh_md5sums -pbedtools
chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
dpkg-deb -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_amd64.deb'.
- dpkg-genchanges >../bedtools_2.17.0-1_amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.19.0-1_amd64.deb'.
+ dpkg-genchanges >../bedtools_2.19.0-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build bedtools-2.17.0
+ dpkg-source --after-build bedtools-2.19.0
+dpkg-source: info: using options from bedtools-2.19.0/debian/source/options: --single-debian-patch
+dpkg-source: info: unapplying debian-changes
dpkg-source: info: unapplying gzstream.h.patch
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121104-1804
+Build finished at 20140216-1610
Finished
────────
@@ -776,71 +915,297 @@ 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-Xd26gd/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:
+ 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
+ libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
+ patchutils t1utils
+Suggested packages:
+ libwww-perl binutils-multiarch libtext-template-perl libyaml-perl
+Recommended packages:
+ libauthen-sasl-perl libhtml-parser-perl libhtml-template-perl
+ libxml-simple-perl libperlio-gzip-perl ifupdown
+The following NEW packages will be installed:
+ 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
+ libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
+ patchutils sbuild-build-depends-lintian-dummy t1utils
+0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
+Need to get 97.3 kB/2492 kB of archives.
+After this operation, 8210 kB of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main libio-socket-ssl-perl all 1.967-1 [97.3 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 97.3 kB in 0s (512 kB/s)
+Selecting previously unselected package netbase.
+(Reading database ... 13627 files and directories currently installed.)
+Preparing to unpack .../archives/netbase_5.2_all.deb ...
+Unpacking netbase (5.2) ...
+Selecting previously unselected package hardening-includes.
+Preparing to unpack .../hardening-includes_2.5_all.deb ...
+Unpacking hardening-includes (2.5) ...
+Selecting previously unselected package libapt-pkg-perl.
+Preparing to unpack .../libapt-pkg-perl_0.1.29+b1_amd64.deb ...
+Unpacking libapt-pkg-perl (0.1.29+b1) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.30-7_all.deb ...
+Unpacking libarchive-zip-perl (1.30-7) ...
+Selecting previously unselected package libsub-name-perl.
+Preparing to unpack .../libsub-name-perl_0.05-1+b3_amd64.deb ...
+Unpacking libsub-name-perl (0.05-1+b3) ...
+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_0.36-1_amd64.deb ...
+Unpacking libclone-perl (0.36-1) ...
+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_1.58-1_amd64.deb ...
+Unpacking libnet-ssleay-perl (1.58-1) ...
+Selecting previously unselected package libio-socket-ssl-perl.
+Preparing to unpack .../libio-socket-ssl-perl_1.967-1_all.deb ...
+Unpacking libio-socket-ssl-perl (1.967-1) ...
+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_2.12-1_all.deb ...
+Unpacking libmailtools-perl (2.12-1) ...
+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 libsocket6-perl.
+Preparing to unpack .../libsocket6-perl_0.23+ds-0+nmu1_amd64.deb ...
+Unpacking libsocket6-perl (0.23+ds-0+nmu1) ...
+Selecting previously unselected package libio-socket-inet6-perl.
+Preparing to unpack .../libio-socket-inet6-perl_2.71-1_all.deb ...
+Unpacking libio-socket-inet6-perl (2.71-1) ...
+Selecting previously unselected package libnet-dns-perl.
+Preparing to unpack .../libnet-dns-perl_0.68-1.2_amd64.deb ...
+Unpacking libnet-dns-perl (0.68-1.2) ...
+Selecting previously unselected package libnet-domain-tld-perl.
+Preparing to unpack .../libnet-domain-tld-perl_1.70-1_all.deb ...
+Unpacking libnet-domain-tld-perl (1.70-1) ...
+Selecting previously unselected package libemail-valid-perl.
+Preparing to unpack .../libemail-valid-perl_1.192-1_all.deb ...
+Unpacking libemail-valid-perl (1.192-1) ...
+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+b3_amd64.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b3) ...
+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_0.33-1+b2_amd64.deb ...
+Unpacking liblist-moreutils-perl (0.33-1+b2) ...
+Selecting previously unselected package libparse-debianchangelog-perl.
+Preparing to unpack .../libparse-debianchangelog-perl_1.2.0-1_all.deb ...
+Unpacking libparse-debianchangelog-perl (1.2.0-1) ...
+Selecting previously unselected package libtext-levenshtein-perl.
+Preparing to unpack .../libtext-levenshtein-perl_0.06~01-2_all.deb ...
+Unpacking libtext-levenshtein-perl (0.06~01-2) ...
+Selecting previously unselected package liburi-perl.
+Preparing to unpack .../liburi-perl_1.60-1_all.deb ...
+Unpacking liburi-perl (1.60-1) ...
+Selecting previously unselected package patchutils.
+Preparing to unpack .../patchutils_0.3.2-3_amd64.deb ...
+Unpacking patchutils (0.3.2-3) ...
+Selecting previously unselected package t1utils.
+Preparing to unpack .../t1utils_1.37-2_amd64.deb ...
+Unpacking t1utils (1.37-2) ...
+Selecting previously unselected package lintian.
+Preparing to unpack .../lintian_2.5.21_all.deb ...
+Unpacking lintian (2.5.21) ...
+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 (2.6.6-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up netbase (5.2) ...
+Setting up hardening-includes (2.5) ...
+Setting up libapt-pkg-perl (0.1.29+b1) ...
+Setting up libarchive-zip-perl (1.30-7) ...
+Setting up libsub-name-perl (0.05-1+b3) ...
+Setting up libclass-accessor-perl (0.34-1) ...
+Setting up libclone-perl (0.36-1) ...
+Setting up libdigest-hmac-perl (1.03+dfsg-1) ...
+Setting up libnet-ssleay-perl (1.58-1) ...
+Setting up libio-socket-ssl-perl (1.967-1) ...
+Setting up libnet-smtp-ssl-perl (1.01-3) ...
+Setting up libmailtools-perl (2.12-1) ...
+Setting up libnet-ip-perl (1.26-1) ...
+Setting up libsocket6-perl (0.23+ds-0+nmu1) ...
+Setting up libio-socket-inet6-perl (2.71-1) ...
+Setting up libnet-dns-perl (0.68-1.2) ...
+Setting up libnet-domain-tld-perl (1.70-1) ...
+Setting up libemail-valid-perl (1.192-1) ...
+Setting up libfile-basedir-perl (0.03-1) ...
+Setting up libio-pty-perl (1:1.08-1+b3) ...
+Setting up libio-string-perl (1.08-3) ...
+Setting up libipc-run-perl (0.92-1) ...
+Setting up liblist-moreutils-perl (0.33-1+b2) ...
+Setting up libparse-debianchangelog-perl (1.2.0-1) ...
+Setting up libtext-levenshtein-perl (0.06~01-2) ...
+Setting up liburi-perl (1.60-1) ...
+Setting up patchutils (0.3.2-3) ...
+Setting up t1utils (1.37-2) ...
+Setting up lintian (2.5.21) ...
+Setting up sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+I: bedtools source: quilt-patch-using-template-description debian-changes
+P: bedtools source: debian-watch-may-check-gpg-signature
+I: bedtools: hardening-no-fortify-functions usr/bin/bedtools
+W: bedtools: binary-without-manpage usr/bin/annotateBed
+W: bedtools: binary-without-manpage usr/bin/bamToBed
+W: bedtools: binary-without-manpage usr/bin/bamToFastq
+W: bedtools: binary-without-manpage usr/bin/bed12ToBed6
+W: bedtools: binary-without-manpage usr/bin/bedToBam
+W: bedtools: binary-without-manpage usr/bin/bedToIgv
+W: bedtools: binary-without-manpage usr/bin/bedpeToBam
+W: bedtools: binary-without-manpage usr/bin/bedtools
+W: bedtools: binary-without-manpage usr/bin/closestBed
+W: bedtools: binary-without-manpage usr/bin/clusterBed
+W: bedtools: binary-without-manpage usr/bin/complementBed
+W: bedtools: binary-without-manpage usr/bin/coverageBed
+W: bedtools: binary-without-manpage usr/bin/expandCols
+W: bedtools: binary-without-manpage usr/bin/fastaFromBed
+W: bedtools: binary-without-manpage usr/bin/flankBed
+W: bedtools: binary-without-manpage usr/bin/genomeCoverageBed
+W: bedtools: binary-without-manpage usr/bin/getOverlap
+W: bedtools: binary-without-manpage usr/bin/intersectBed
+W: bedtools: binary-without-manpage usr/bin/linksBed
+W: bedtools: binary-without-manpage usr/bin/mapBed
+W: bedtools: binary-without-manpage usr/bin/maskFastaFromBed
+W: bedtools: binary-without-manpage usr/bin/mergeBed
+W: bedtools: binary-without-manpage usr/bin/multiBamCov
+W: bedtools: binary-without-manpage usr/bin/multiIntersectBed
+W: bedtools: binary-without-manpage usr/bin/nucBed
+W: bedtools: binary-without-manpage usr/bin/pairToBed
+W: bedtools: binary-without-manpage usr/bin/pairToPair
+W: bedtools: binary-without-manpage usr/bin/randomBed
+W: bedtools: binary-without-manpage usr/bin/shuffleBed
+W: bedtools: binary-without-manpage usr/bin/slopBed
+W: bedtools: binary-without-manpage usr/bin/sortBed
+W: bedtools: binary-without-manpage usr/bin/subtractBed
+W: bedtools: binary-without-manpage usr/bin/tagBam
+W: bedtools: binary-without-manpage usr/bin/unionBedGraphs
+W: bedtools: binary-without-manpage usr/bin/windowBed
+W: bedtools: binary-without-manpage usr/bin/windowMaker
+W: bedtools: executable-not-elf-or-script usr/share/bedtools/genomes/human.hg19.genome
+W: bedtools: executable-not-elf-or-script usr/share/bedtools/genomes/human.hg18.genome
+W: bedtools: executable-not-elf-or-script usr/share/bedtools/genomes/mouse.mm8.genome
+W: bedtools: executable-not-elf-or-script usr/share/bedtools/genomes/mouse.mm9.genome
+W: bedtools: executable-not-elf-or-script usr/share/bedtools/test/intersect/new_test-intersect.sh
+W: bedtools: executable-not-elf-or-script usr/share/bedtools/test/intersect/performanceTest.sh
+
+I: Lintian run was successful.
+
+┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.17.0-1_amd64.changes:
+bedtools_2.19.0-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Sun, 04 Nov 2012 17:59:41 +0900
+Date: Sat, 15 Feb 2014 19:39:23 +0900
Source: bedtools
Binary: bedtools
Architecture: source amd64
-Version: 2.17.0-1
+Version: 2.19.0-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
+Closes: 714873
Changes:
- bedtools (2.17.0-1) unstable; urgency=low
+ bedtools (2.19.0-1) unstable; urgency=low
.
- bb9012e Imported Upstream version 2.16.2.
- 9006b23 Imported Upstream version 2.17.0.
- 9112569 Documented BEDTools license as a whole.
- 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
- a781b14 Conforms with Policy 3.9.4.
- 84b1167 Use Debhelper 9.
- 0bf572d Distribute the test suite.
- 422cd34 Bash completion for BEDTools.
+ e07e70c Imported Upstream version 2.19.0
+ afdc61a Watch GitHub at https://github.com/arq5x/bedtools2.
+ 4abe14e Source control file normalised with config-model-edit.
+ 0518353 Corrected a typo in the long description. (Closes: #714873)
+ f63d85e Follow the layout of the upstream repository.
+ c25f9e5 Correct name of README file in debian/docs.
+ 5561c7c Emulate source format 1.0 in the format 3.0 (quilt).
+ a45a0ab Canonical VCS URLs.
+ 4459dfe Conforms with Policy 3.9.5.
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+ b844b6f14b50dd45c39b48ae7e593da8 554664 science optional bedtools_2.19.0-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.17.0-1_amd64.deb
+bedtools_2.19.0-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 442978 bytes: control archive=4102 bytes.
+ size 554664 bytes: control archive=6287 bytes.
32 bytes, 1 lines conffiles
- 833 bytes, 18 lines control
- 9605 bytes, 132 lines md5sums
+ 835 bytes, 18 lines control
+ 14686 bytes, 194 lines md5sums
Package: bedtools
- Version: 2.17.0-1
+ Version: 2.19.0-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1406
- Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
+ Installed-Size: 2341
+ Depends: libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -852,170 +1217,234 @@ bedtools_2.17.0-1_amd64.deb
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
.
- The groupBy utility is distribued in the filo package.
+ The groupBy utility is distributed in the filo package.
-drwxr-xr-x root/root 0 2012-11-04 18:04 ./
-drwxr-xr-x root/root 0 2012-11-04 18:04 ./etc/
-drwxr-xr-x root/root 0 2012-11-04 18:04 ./etc/bash_completion.d/
--rw-r--r-- root/root 638 2012-11-04 17:54 ./etc/bash_completion.d/bedtools
-drwxr-xr-x root/root 0 2012-11-04 18:04 ./usr/
-drwxr-xr-x root/root 0 2012-11-04 18:04 ./usr/bin/
--rwxr-xr-x root/root 1351312 2012-11-04 18:04 ./usr/bin/bedtools
--rwxr-xr-x root/root 44 2012-11-04 18:04 ./usr/bin/windowMaker
--rwxr-xr-x root/root 39 2012-11-04 18:04 ./usr/bin/windowBed
--rwxr-xr-x root/root 42 2012-11-04 18:04 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 36 2012-11-04 18:04 ./usr/bin/tagBam
--rwxr-xr-x root/root 41 2012-11-04 18:04 ./usr/bin/subtractBed
--rwxr-xr-x root/root 37 2012-11-04 18:04 ./usr/bin/sortBed
--rwxr-xr-x root/root 37 2012-11-04 18:04 ./usr/bin/slopBed
--rwxr-xr-x root/root 40 2012-11-04 18:04 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 39 2012-11-04 18:04 ./usr/bin/randomBed
--rwxr-xr-x root/root 43 2012-11-04 18:04 ./usr/bin/pairToPair
--rwxr-xr-x root/root 42 2012-11-04 18:04 ./usr/bin/pairToBed
--rwxr-xr-x root/root 36 2012-11-04 18:04 ./usr/bin/nucBed
--rwxr-xr-x root/root 43 2012-11-04 18:04 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 41 2012-11-04 18:04 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 38 2012-11-04 18:04 ./usr/bin/mergeBed
--rwxr-xr-x root/root 42 2012-11-04 18:04 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 36 2012-11-04 18:04 ./usr/bin/mapBed
--rwxr-xr-x root/root 38 2012-11-04 18:04 ./usr/bin/linksBed
--rwxr-xr-x root/root 42 2012-11-04 18:04 ./usr/bin/intersectBed
--rwxr-xr-x root/root 40 2012-11-04 18:04 ./usr/bin/getOverlap
--rwxr-xr-x root/root 42 2012-11-04 18:04 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 38 2012-11-04 18:04 ./usr/bin/flankBed
--rwxr-xr-x root/root 41 2012-11-04 18:04 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 39 2012-11-04 18:04 ./usr/bin/expandCols
--rwxr-xr-x root/root 41 2012-11-04 18:04 ./usr/bin/coverageBed
--rwxr-xr-x root/root 43 2012-11-04 18:04 ./usr/bin/complementBed
--rwxr-xr-x root/root 40 2012-11-04 18:04 ./usr/bin/clusterBed
--rwxr-xr-x root/root 40 2012-11-04 18:04 ./usr/bin/closestBed
--rwxr-xr-x root/root 36 2012-11-04 18:04 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 41 2012-11-04 18:04 ./usr/bin/bedToBam
--rwxr-xr-x root/root 43 2012-11-04 18:04 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 44 2012-11-04 18:04 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 43 2012-11-04 18:04 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 41 2012-11-04 18:04 ./usr/bin/bamToBed
--rwxr-xr-x root/root 41 2012-11-04 18:04 ./usr/bin/annotateBed
-drwxr-xr-x root/root 0 2012-11-04 18:04 ./usr/share/
-drwxr-xr-x root/root 0 2012-11-04 18:04 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-11-04 18:04 ./usr/share/bedtools/test/
--rw-r--r-- root/root 1243 2012-11-04 02:11 ./usr/share/bedtools/test/test.sh
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/subtract/
--rw-r--r-- root/root 36 2012-11-04 02:11 ./usr/share/bedtools/test/subtract/a.bed
--rw-r--r-- root/root 36 2012-11-04 02:11 ./usr/share/bedtools/test/subtract/b.bed
--rw-r--r-- root/root 2532 2012-11-04 02:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/slop/
--rw-r--r-- root/root 41 2012-11-04 02:11 ./usr/share/bedtools/test/slop/a.bed
--rw-r--r-- root/root 3603 2012-11-04 02:11 ./usr/share/bedtools/test/slop/test-slop.sh
--rw-r--r-- root/root 10 2012-11-04 02:11 ./usr/share/bedtools/test/slop/tiny.genome
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/multicov/
--rw-r--r-- root/root 72 2012-11-04 02:11 ./usr/share/bedtools/test/multicov/multicov.bed
--rw-r--r-- root/root 96 2012-11-04 02:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
--rw-r--r-- root/root 162 2012-11-04 02:11 ./usr/share/bedtools/test/multicov/one_block.sam
--rw-r--r-- root/root 3836 2012-11-04 02:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
--rw-r--r-- root/root 96 2012-11-04 02:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
--rw-r--r-- root/root 167 2012-11-04 02:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/merge/
--rw-r--r-- root/root 46 2012-11-04 02:11 ./usr/share/bedtools/test/merge/a.bed
--rw-r--r-- root/root 147 2012-11-04 02:11 ./usr/share/bedtools/test/merge/a.full.bed
--rw-r--r-- root/root 57 2012-11-04 02:11 ./usr/share/bedtools/test/merge/a.names.bed
--rw-r--r-- root/root 3642 2012-11-04 02:11 ./usr/share/bedtools/test/merge/test-merge.sh
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/map/
--rw-r--r-- root/root 72 2012-11-04 02:11 ./usr/share/bedtools/test/map/ivls.bed
--rw-r--r-- root/root 2753 2012-11-04 02:11 ./usr/share/bedtools/test/map/test-map.sh
--rw-r--r-- root/root 147 2012-11-04 02:11 ./usr/share/bedtools/test/map/values.bed
--rw-r--r-- root/root 186 2012-11-04 02:11 ./usr/share/bedtools/test/map/values2.bed
--rw-r--r-- root/root 227 2012-11-04 02:11 ./usr/share/bedtools/test/map/values3.bed
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/jaccard/
--rw-r--r-- root/root 38 2012-11-04 02:11 ./usr/share/bedtools/test/jaccard/a.bed
--rw-r--r-- root/root 77 2012-11-04 02:11 ./usr/share/bedtools/test/jaccard/b.bed
--rw-r--r-- root/root 18 2012-11-04 02:11 ./usr/share/bedtools/test/jaccard/c.bed
--rw-r--r-- root/root 11 2012-11-04 02:11 ./usr/share/bedtools/test/jaccard/d.bed
--rw-r--r-- root/root 825 2012-11-04 02:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/intersect/
--rw-r--r-- root/root 38 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/a.bed
--rw-r--r-- root/root 76 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/b.bed
--rw-r--r-- root/root 18 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/c.bed
--rw-r--r-- root/root 255 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
--rw-r--r-- root/root 162 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/one_block.sam
--rw-r--r-- root/root 10172 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
--rw-r--r-- root/root 176 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
--rw-r--r-- root/root 60 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
--rw-r--r-- root/root 63 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
--rw-r--r-- root/root 63 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
--rw-r--r-- root/root 167 2012-11-04 02:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/groupBy/
--rw-r--r-- root/root 885 2012-11-04 02:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
--rw-r--r-- root/root 250 2012-11-04 02:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
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--rw-r--r-- root/root 117 2012-11-04 02:11 ./usr/share/bedtools/test/getfasta/blocks.bed
--rw-r--r-- root/root 0 2012-11-04 02:11 ./usr/share/bedtools/test/getfasta/t.bed
--rw-r--r-- root/root 61 2012-11-04 02:11 ./usr/share/bedtools/test/getfasta/t.fa
--rw-r--r-- root/root 16 2012-11-04 02:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
--rw-r--r-- root/root 1193 2012-11-04 02:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/genomecov/
--rw-r--r-- root/root 156 2012-11-04 02:11 ./usr/share/bedtools/test/genomecov/one_block.sam
--rw-r--r-- root/root 142 2012-11-04 02:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
--rw-r--r-- root/root 3402 2012-11-04 02:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
--rw-r--r-- root/root 171 2012-11-04 02:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
--rw-r--r-- root/root 60 2012-11-04 02:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
--rw-r--r-- root/root 63 2012-11-04 02:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
--rw-r--r-- root/root 63 2012-11-04 02:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
--rw-r--r-- root/root 162 2012-11-04 02:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
-drwxr-xr-x root/root 0 2012-11-04 18:01 ./usr/share/bedtools/test/general/
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+-rw-r--r-- root/root 1453 2014-02-09 11:29 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2014-02-09 11:29 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 3865 2014-02-09 11:29 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 41 2014-02-09 11:29 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 10 2014-02-09 11:29 ./usr/share/bedtools/test/flank/tiny.genome
+drwxr-xr-x root/root 0 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 63 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 142 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 3408 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 63 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 156 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 162 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+-rw-r--r-- root/root 60 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 171 2014-02-09 11:29 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+drwxr-xr-x root/root 0 2014-02-09 11:29 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 3842 2014-02-09 11:29 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 96 2014-02-09 11:29 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 96 2014-02-09 11:29 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+-rw-r--r-- root/root 72 2014-02-09 11:29 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 162 2014-02-09 11:29 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 167 2014-02-09 11:29 ./usr/share/bedtools/test/multicov/two_blocks.sam
+drwxr-xr-x root/root 0 2014-02-09 11:29 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 43 2014-02-09 11:29 ./usr/share/bedtools/test/getfasta/t_fH.fa.fai
+-rw-r--r-- root/root 117 2014-02-09 11:29 ./usr/share/bedtools/test/getfasta/blocks.bed
+-rw-r--r-- root/root 1698 2014-02-09 11:29 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+-rw-r--r-- root/root 0 2014-02-09 11:29 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 16 2014-02-09 11:29 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 87 2014-02-09 11:29 ./usr/share/bedtools/test/getfasta/t_fH.fa
+-rw-r--r-- root/root 61 2014-02-09 11:29 ./usr/share/bedtools/test/getfasta/t.fa
+drwxr-xr-x root/root 0 2014-02-09 11:29 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 41 2014-02-09 11:29 ./usr/share/bedtools/test/slop/a.bed
+-rw-r--r-- root/root 3609 2014-02-09 11:29 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 10 2014-02-09 11:29 ./usr/share/bedtools/test/slop/tiny.genome
+drwxr-xr-x root/root 0 2014-02-16 16:10 ./usr/bin/
+-rwxr-xr-x root/root 41 2014-02-16 16:10 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 38 2014-02-16 16:10 ./usr/bin/linksBed
+-rwxr-xr-x root/root 36 2014-02-16 16:10 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 38 2014-02-16 16:10 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 36 2014-02-16 16:10 ./usr/bin/mapBed
+-rwxr-xr-x root/root 41 2014-02-16 16:10 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 42 2014-02-16 16:10 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 41 2014-02-16 16:10 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 43 2014-02-16 16:10 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 40 2014-02-16 16:10 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 44 2014-02-16 16:10 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 43 2014-02-16 16:10 ./usr/bin/complementBed
+-rwxr-xr-x root/root 43 2014-02-16 16:10 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 42 2014-02-16 16:10 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 41 2014-02-16 16:10 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 37 2014-02-16 16:10 ./usr/bin/slopBed
+-rwxr-xr-x root/root 42 2014-02-16 16:10 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 39 2014-02-16 16:10 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2014-02-16 16:10 ./usr/bin/nucBed
+-rwxr-xr-x root/root 43 2014-02-16 16:10 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 38 2014-02-16 16:10 ./usr/bin/flankBed
+-rwxr-xr-x root/root 41 2014-02-16 16:10 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 44 2014-02-16 16:10 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 39 2014-02-16 16:10 ./usr/bin/randomBed
+-rwxr-xr-x root/root 1654464 2014-02-16 16:10 ./usr/bin/bedtools
+-rwxr-xr-x root/root 42 2014-02-16 16:10 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 41 2014-02-16 16:10 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 41 2014-02-16 16:10 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 40 2014-02-16 16:10 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 39 2014-02-16 16:10 ./usr/bin/expandCols
+-rwxr-xr-x root/root 40 2014-02-16 16:10 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 42 2014-02-16 16:10 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 40 2014-02-16 16:10 ./usr/bin/closestBed
+-rwxr-xr-x root/root 37 2014-02-16 16:10 ./usr/bin/sortBed
+-rwxr-xr-x root/root 43 2014-02-16 16:10 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 36 2014-02-16 16:10 ./usr/bin/tagBam
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1023,82 +1452,150 @@ drwxr-xr-x root/root 0 2012-11-04 18:04 ./usr/share/doc/bedtools/
└──────────────────────────────────────────────────────────────────────────────┘
-lintian
-───────
-
-P: bedtools source: unneeded-build-dep-on-quilt
-W: bedtools source: newer-standards-version 3.9.4 (current is 3.9.3)
-W: bedtools: hardening-no-fortify-functions usr/bin/bedtools
-P: bedtools: data.tar.xz-member-without-dpkg-pre-depends
-W: bedtools: binary-without-manpage usr/bin/annotateBed
-W: bedtools: binary-without-manpage usr/bin/bamToBed
-W: bedtools: binary-without-manpage usr/bin/bamToFastq
-W: bedtools: binary-without-manpage usr/bin/bed12ToBed6
-W: bedtools: binary-without-manpage usr/bin/bedToBam
-W: bedtools: binary-without-manpage usr/bin/bedToIgv
-W: bedtools: binary-without-manpage usr/bin/bedpeToBam
-W: bedtools: binary-without-manpage usr/bin/bedtools
-W: bedtools: binary-without-manpage usr/bin/closestBed
-W: bedtools: binary-without-manpage usr/bin/clusterBed
-W: bedtools: binary-without-manpage usr/bin/complementBed
-W: bedtools: binary-without-manpage usr/bin/coverageBed
-W: bedtools: binary-without-manpage usr/bin/expandCols
-W: bedtools: binary-without-manpage usr/bin/fastaFromBed
-W: bedtools: binary-without-manpage usr/bin/flankBed
-W: bedtools: binary-without-manpage usr/bin/genomeCoverageBed
-W: bedtools: binary-without-manpage usr/bin/getOverlap
-W: bedtools: binary-without-manpage usr/bin/intersectBed
-W: bedtools: binary-without-manpage usr/bin/linksBed
-W: bedtools: binary-without-manpage usr/bin/mapBed
-W: bedtools: binary-without-manpage usr/bin/maskFastaFromBed
-W: bedtools: binary-without-manpage usr/bin/mergeBed
-W: bedtools: binary-without-manpage usr/bin/multiBamCov
-W: bedtools: binary-without-manpage usr/bin/multiIntersectBed
-W: bedtools: binary-without-manpage usr/bin/nucBed
-W: bedtools: binary-without-manpage usr/bin/pairToBed
-W: bedtools: binary-without-manpage usr/bin/pairToPair
-W: bedtools: binary-without-manpage usr/bin/randomBed
-W: bedtools: binary-without-manpage usr/bin/shuffleBed
-W: bedtools: binary-without-manpage usr/bin/slopBed
-W: bedtools: binary-without-manpage usr/bin/sortBed
-W: bedtools: binary-without-manpage usr/bin/subtractBed
-W: bedtools: binary-without-manpage usr/bin/tagBam
-W: bedtools: binary-without-manpage usr/bin/unionBedGraphs
-W: bedtools: binary-without-manpage usr/bin/windowBed
-W: bedtools: binary-without-manpage usr/bin/windowMaker
-W: bedtools: executable-not-elf-or-script usr/share/bedtools/genomes/human.hg18.genome
-W: bedtools: executable-not-elf-or-script usr/share/bedtools/genomes/mouse.mm9.genome
-W: bedtools: executable-not-elf-or-script usr/share/bedtools/genomes/human.hg19.genome
-W: bedtools: executable-not-elf-or-script usr/share/bedtools/genomes/mouse.mm8.genome
-
-I: Lintian run was successful.
-
┌──────────────────────────────────────────────────────────────────────────────┐
│ 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:
+ bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base*
+ groff-base* hardening-includes* intltool-debian* libapt-pkg-perl*
+ libarchive-zip-perl* libasprintf0c2* libclass-accessor-perl* libclone-perl*
+ libcroco3* libdigest-hmac-perl* libemail-valid-perl* libexpat1* libffi6*
+ libfile-basedir-perl* libglib2.0-0* libio-pty-perl* libio-socket-inet6-perl*
+ libio-socket-ssl-perl* libio-string-perl* libipc-run-perl*
+ liblist-moreutils-perl* libmagic1* libmailtools-perl* libncursesw5*
+ libnet-dns-perl* libnet-domain-tld-perl* libnet-ip-perl*
+ libnet-smtp-ssl-perl* libnet-ssleay-perl* libparse-debianchangelog-perl*
+ libpipeline1* libpython-stdlib* libpython2.7-minimal* libpython2.7-stdlib*
+ libsocket6-perl* libsqlite3-0* libssl1.0.0* libsub-name-perl*
+ libtext-levenshtein-perl* libunistring0* liburi-perl* libxml2* lintian*
+ man-db* mime-support* netbase* patchutils* po-debconf* python*
+ python-minimal* python2.7* python2.7-minimal* quilt*
+ sbuild-build-depends-bedtools-dummy* sbuild-build-depends-core-dummy*
+ sbuild-build-depends-lintian-dummy* t1utils* zlib1g-dev*
+0 upgraded, 0 newly installed, 65 to remove and 0 not upgraded.
+After this operation, 56.1 MB disk space will be freed.
+(Reading database ... 14800 files and directories currently installed.)
+Removing sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
+Removing quilt (0.61-1) ...
+Purging configuration files for quilt (0.61-1) ...
+Removing sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Removing lintian (2.5.21) ...
+Purging configuration files for lintian (2.5.21) ...
+Removing cdbs (0.4.122) ...
+Removing debhelper (9.20131227) ...
+Removing diffstat (1.58-1) ...
+Removing file (1:5.14-2) ...
+Removing po-debconf (1.0.16+nmu2) ...
+Removing intltool-debian (0.35.0+20060710.1) ...
+Removing gettext (0.18.3.2-1) ...
+Removing gettext-base (0.18.3.2-1) ...
+Removing hardening-includes (2.5) ...
+Removing libapt-pkg-perl (0.1.29+b1) ...
+Removing libarchive-zip-perl (1.30-7) ...
+Removing libasprintf0c2:amd64 (0.18.3.2-1) ...
+Removing libparse-debianchangelog-perl (1.2.0-1) ...
+Removing libclass-accessor-perl (0.34-1) ...
+Removing libclone-perl (0.36-1) ...
+Removing libcroco3:amd64 (0.6.8-2) ...
+Purging configuration files for libcroco3:amd64 (0.6.8-2) ...
+Removing libemail-valid-perl (1.192-1) ...
+Removing libnet-dns-perl (0.68-1.2) ...
+Removing libdigest-hmac-perl (1.03+dfsg-1) ...
+Removing python (2.7.5-5) ...
+Purging configuration files for python (2.7.5-5) ...
+Removing python2.7 (2.7.6-5) ...
+Purging configuration files for python2.7 (2.7.6-5) ...
+Removing libpython-stdlib:amd64 (2.7.5-5) ...
+Removing libpython2.7-stdlib:amd64 (2.7.6-5) ...
+dpkg-query: no packages found matching pkgname
+Removing libexpat1:amd64 (2.1.0-4) ...
+Purging configuration files for libexpat1:amd64 (2.1.0-4) ...
+Removing libglib2.0-0:amd64 (2.38.2-5) ...
+Purging configuration files for libglib2.0-0:amd64 (2.38.2-5) ...
+Removing libffi6:amd64 (3.0.13-12) ...
+Purging configuration files for libffi6:amd64 (3.0.13-12) ...
+Removing libfile-basedir-perl (0.03-1) ...
+Removing libipc-run-perl (0.92-1) ...
+Removing libio-pty-perl (1:1.08-1+b3) ...
+Removing libio-socket-inet6-perl (2.71-1) ...
+Removing libmailtools-perl (2.12-1) ...
+Removing libnet-smtp-ssl-perl (1.01-3) ...
+Removing libio-socket-ssl-perl (1.967-1) ...
+Removing libio-string-perl (1.08-3) ...
+Removing liblist-moreutils-perl (0.33-1+b2) ...
+Removing libmagic1:amd64 (1:5.14-2) ...
+Purging configuration files for libmagic1:amd64 (1:5.14-2) ...
+Removing libncursesw5:amd64 (5.9+20140118-1) ...
+Purging configuration files for libncursesw5:amd64 (5.9+20140118-1) ...
+Removing libnet-domain-tld-perl (1.70-1) ...
+Removing libnet-ip-perl (1.26-1) ...
+Removing libnet-ssleay-perl (1.58-1) ...
+Removing python-minimal (2.7.5-5) ...
+Removing python2.7-minimal (2.7.6-5) ...
+Purging configuration files for python2.7-minimal (2.7.6-5) ...
+Removing libpython2.7-minimal:amd64 (2.7.6-5) ...
+dpkg-query: no packages found matching pkgname
+dpkg-query: no packages found matching pkgname
+Purging configuration files for libpython2.7-minimal:amd64 (2.7.6-5) ...
+dpkg-query: no packages found matching pkgname
+Removing libsocket6-perl (0.23+ds-0+nmu1) ...
+Removing libsqlite3-0:amd64 (3.8.3.1-1) ...
+Purging configuration files for libsqlite3-0:amd64 (3.8.3.1-1) ...
+Removing libssl1.0.0:amd64 (1.0.1f-1) ...
+Purging configuration files for libssl1.0.0:amd64 (1.0.1f-1) ...
+Removing libsub-name-perl (0.05-1+b3) ...
+Removing libtext-levenshtein-perl (0.06~01-2) ...
+Removing libunistring0:amd64 (0.9.3-5) ...
+Purging configuration files for libunistring0:amd64 (0.9.3-5) ...
+Removing liburi-perl (1.60-1) ...
+Removing libxml2:amd64 (2.9.1+dfsg1-3) ...
+Purging configuration files for libxml2:amd64 (2.9.1+dfsg1-3) ...
+Removing mime-support (3.54) ...
+Purging configuration files for mime-support (3.54) ...
+Removing netbase (5.2) ...
+Purging configuration files for netbase (5.2) ...
+Removing patchutils (0.3.2-3) ...
+Removing sbuild-build-depends-core-dummy (0.invalid.0) ...
+Removing t1utils (1.37-2) ...
+Removing zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ...
+Removing man-db (2.6.6-1) ...
+Purging configuration files for man-db (2.6.6-1) ...
+Removing bsdmainutils (9.0.5) ...
+Purging configuration files for bsdmainutils (9.0.5) ...
+Removing groff-base (1.22.2-5) ...
+Purging configuration files for groff-base (1.22.2-5) ...
+Removing libpipeline1:amd64 (1.2.6-2) ...
+Purging configuration files for libpipeline1:amd64 (1.2.6-2) ...
+Processing triggers for libc-bin (2.17-97) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: amd64
-Build-Space: 118408
-Build-Time: 188
+Build-Space: 157668
+Build-Time: 250
Distribution: unstable
Host Architecture: amd64
-Install-Time: 34
-Job: bedtools_2.17.0-1.dsc
+Install-Time: 23
+Job: bedtools_2.19.0-1.dsc
Lintian: pass
Machine Architecture: amd64
Package: bedtools
-Package-Time: 234
-Source-Version: 2.17.0-1
-Space: 118408
+Package-Time: 281
+Source-Version: 2.19.0-1
+Space: 157668
Status: successful
-Version: 2.17.0-1
+Version: 2.19.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121104-1804
-Build needed 00:03:54, 118408k disc space
+Finished at 20140216-1610
+Build needed 00:04:41, 157668k disc space
diff --git a/dsc b/dsc
index 57fc44d..9160b21 100644
--- a/dsc
+++ b/dsc
@@ -1,44 +1,44 @@
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-Hash: SHA256
+Hash: SHA512
Format: 3.0 (quilt)
Source: bedtools
Binary: bedtools
Architecture: any
-Version: 2.17.0-1
+Version: 2.19.0-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>
Homepage: http://code.google.com/p/bedtools/
-Standards-Version: 3.9.4
-Vcs-Browser: http://git.debian.org/?p=debian-med/bedtools.git
-Vcs-Git: git://git.debian.org/debian-med/bedtools.git
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/bedtools.git
+Vcs-Git: git://anonscm.debian.org/debian-med/bedtools.git
Build-Depends: cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Package-List:
bedtools deb science optional
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-----END PGP SIGNATURE-----
diff --git a/upload b/upload
index a0d98c4..153e86a 100644
--- a/upload
+++ b/upload
@@ -1,6 +1,6 @@
-u bedtools_2.17.0-1_amd64.deb ftp.upload.debian.org Sun Nov 4 18:09:53 2012
-u bedtools_2.17.0-1.debian.tar.gz ftp.upload.debian.org Sun Nov 4 18:09:54 2012
-u bedtools_2.17.0.orig.tar.gz ftp.upload.debian.org Sun Nov 4 18:10:02 2012
-u bedtools_2.17.0-1.dsc ftp.upload.debian.org Sun Nov 4 18:10:03 2012
-u bedtools_2.17.0-1_amd64.changes ftp.upload.debian.org Sun Nov 4 18:10:04 2012
-s bedtools_2.17.0-1_amd64.changes ftp.upload.debian.org Sun Nov 4 18:10:04 2012
+u bedtools_2.19.0.orig.tar.gz ftp.upload.debian.org Sun Feb 16 16:18:14 2014
+u bedtools_2.19.0-1.dsc ftp.upload.debian.org Sun Feb 16 16:18:15 2014
+u bedtools_2.19.0-1_amd64.deb ftp.upload.debian.org Sun Feb 16 16:18:18 2014
+u bedtools_2.19.0-1.debian.tar.xz ftp.upload.debian.org Sun Feb 16 16:18:19 2014
+u bedtools_2.19.0-1_amd64.changes ftp.upload.debian.org Sun Feb 16 16:18:20 2014
+s bedtools_2.19.0-1_amd64.changes ftp.upload.debian.org Sun Feb 16 16:18:20 2014
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git
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