[med-svn] [SCM] cufflinks branch, builds/amd64, updated. builds/amd64/1.2.1-1-1-g3e9d5ad
Charles Plessy
plessy at debian.org
Fri Jan 6 00:37:40 UTC 2012
The following commit has been merged in the builds/amd64 branch:
commit 3e9d5adcc3687ce0da563583ade088bc86853ce5
Author: Charles Plessy <plessy at debian.org>
Date: Fri Jan 6 09:35:36 2012 +0900
Uploaded cufflinks_1.3.0-1_amd64.changes.
diff --git a/changes b/changes
index dc9e3fa..f9e15a4 100644
--- a/changes
+++ b/changes
@@ -2,92 +2,57 @@
Hash: SHA256
Format: 1.8
-Date: Sun, 11 Dec 2011 12:07:02 +0900
+Date: Fri, 06 Jan 2012 09:20:23 +0900
Source: cufflinks
Binary: cufflinks
Architecture: source amd64
-Version: 1.2.1-1
+Version: 1.3.0-1
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:
cufflinks - Transcript assembly, differential expression and regulation for R
-Closes: 627799
Changes:
- cufflinks (1.2.1-1) unstable; urgency=low
+ cufflinks (1.3.0-1) unstable; urgency=low
.
[ Alexandre Mestiashvili ]
* New upstream release
- * added patch to fix bam.h location .
- * debian/rules invoke autoreconf
- * debian/rules added overrides for dh_auto_clean and dh_clean
- * added missing dependency - quilt .We use dh_quilt_patch,
- dh_quilt_unpatch helpers
- * debian/control added dependency python (>=2.6.6-3~) for source package
- * debian/control added dependency python (>=2.6.6-3~) for binary package
- .
- [ Andreas Tille ]
- * Added myself to uploaders
- * Debhelper 8 (control+compat)
- * debian/watch: removed dh-make template from watch file
- * debian/rules: invoke autotools_dev
- .
- [ Charles Plessy ]
- * Switch to non-free section because of the locfit license (debian/control).
- * Added myself to Uploaders (debian/control).
- * Compress binary package with xz (debian/rules).
- * Pre-depend on dpkg (>= 1.15.6) for xz compression (Ubuntu LTS).
- .
- cufflinks (1.0.3-1) UNRELEASED; urgency=low
- .
- [ Alex Mestiashvili ]
- * added docs
- * added missing dependency
- * libbam-dev provides necessary headers only from 0.1.16 version .
- Fixed in control file.
+ * Fixed spelling error.
+ * Updated source version
.
[ Charles Plessy ]
- * Add debian/gbp.conf to show the package is managed with git-buildpackage.
- * Converted Debian copyright file to machine-readable format (DEP 5).
- * Reviewed copyright and license notices, and found that locfit is non-free…
- .
- [ Alex Mestiashvili ]
- * Imported Upstream version 1.0.3 (bugfix)
- .
- cufflinks (1.0.2-1) UNRELEASED; urgency=low
- .
- * Initial release (Closes: #627799)
+ * Removed quilt patch management, and rely on dpkg-dev exclusively.
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+ 6914059cf8c8f22eb388e1fde44deabe 676660 non-free/science optional cufflinks_1.3.0.orig.tar.gz
+ 44296465461c9626c80056250d8bb018 11608 non-free/science optional cufflinks_1.3.0-1.debian.tar.gz
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diff --git a/dsc b/dsc
index 4c0364e..d9faeec 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: cufflinks
Binary: cufflinks
Architecture: any
-Version: 1.2.1-1
+Version: 1.3.0-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>, Andreas Tille <tille at debian.org>, Charles Plessy <plessy at debian.org>
Dm-Upload-Allowed: yes
@@ -13,33 +13,33 @@ Homepage: http://cufflinks.cbcb.umd.edu/
Standards-Version: 3.9.2
Vcs-Browser: http://git.debian.org/?p=debian-med/cufflinks.git;a=summary
Vcs-Git: git://git.debian.org/debian-med/cufflinks.git
-Build-Depends: debhelper (>= 8), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, quilt (>= 0.46-7~), python (>= 2.6.6-3~)
+Build-Depends: debhelper (>= 8), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python (>= 2.6.6-3~)
Package-List:
cufflinks deb non-free/science optional
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+ fa93a7a33f0649793ec1d185cb7043fd0dc2018b 676660 cufflinks_1.3.0.orig.tar.gz
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Files:
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- f365c08b47ad5400745688ae8224c279 11462 cufflinks_1.2.1-1.debian.tar.gz
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diff --git a/log b/log
index 40be51e..37155c4 100644
--- a/log
+++ b/log
@@ -1,18 +1,18 @@
sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ cufflinks 1.2.1-1 (amd64) 11 déc. 2011 12:41 ║
+║ cufflinks 1.3.0-1 (amd64) 06 janv. 2012 09:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: cufflinks
-Version: 1.2.1-1
-Source Version: 1.2.1-1
+Version: 1.3.0-1
+Source Version: 1.3.0-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/cufflinks-fuJaGG/cufflinks-1.2.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/cufflinks-fuJaGG' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-d2d85a4d-0eaa-49e5-835c-7d630fe7c990' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/cufflinks-NtmIkM/cufflinks-1.3.0' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/cufflinks-NtmIkM' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-48ef29fa-8362-4a84-aa4d-3f35ec1f65b0' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -37,14 +37,14 @@ Reading state information...
Local sources
─────────────
-cufflinks_1.2.1-1.dsc exists in .; copying to chroot
+cufflinks_1.3.0-1.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-1w0ZKY/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-ixoWFD/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -60,15 +60,15 @@ The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/714 B of archives.
+Need to get 0 B/716 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 ... 10811 files and directories currently installed.)
+(Reading database ... 10804 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
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), debhelper (>= 8), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, quilt (>= 0.46-7~), python (>= 2.6.6-3~)
-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), debhelper (>= 8), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, quilt (>= 0.46-7~), python (>= 2.6.6-3~)
-dpkg-deb: building package `sbuild-build-depends-cufflinks-dummy' in `/«BUILDDIR»/resolver-QsozZX/apt_archive/sbuild-build-depends-cufflinks-dummy.deb'.
+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), debhelper (>= 8), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python (>= 2.6.6-3~)
+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), debhelper (>= 8), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python (>= 2.6.6-3~)
+dpkg-deb: building package `sbuild-build-depends-cufflinks-dummy' in `/«BUILDDIR»/resolver-fayVYW/apt_archive/sbuild-build-depends-cufflinks-dummy.deb'.
OK
Reading package lists...
@@ -81,15 +81,15 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf
- diffstat file gettext gettext-base groff-base html2text intltool-debian
- libbam-dev libboost-date-time1.46-dev libboost-date-time1.46.1 libboost-dev
+ autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf file
+ gettext gettext-base groff-base html2text intltool-debian libbam-dev
+ libboost-date-time1.46-dev libboost-date-time1.46.1 libboost-dev
libboost-serialization1.46-dev libboost-serialization1.46.1
libboost-thread-dev libboost-thread1.46-dev libboost-thread1.46.1
libboost1.46-dev libcroco3 libexpat1 libffi5 libglib2.0-0 libicu48 libmagic1
libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libtool
libunistring0 libxml2 m4 man-db mime-support po-debconf python
- python-minimal python2.7 python2.7-minimal quilt zlib1g-dev
+ python-minimal python2.7 python2.7-minimal zlib1g-dev
Suggested packages:
autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist
whois vacation dh-make gettext-doc groff libboost1.46-doc
@@ -100,28 +100,27 @@ Suggested packages:
libboost-signals1.46-dev libboost-system1.46-dev libboost-test1.46-dev
libboost-wave1.46-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk
fop libtool-doc automaken gfortran fortran95-compiler gcj less www-browser
- libmail-box-perl python-doc python-tk python2.7-doc binfmt-support procmail
- graphviz
+ libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
autopoint curl wget lynx-cur libglib2.0-data shared-mime-info libgpm2
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf
- diffstat file gettext gettext-base groff-base html2text intltool-debian
- libbam-dev libboost-date-time1.46-dev libboost-date-time1.46.1 libboost-dev
+ autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf file
+ gettext gettext-base groff-base html2text intltool-debian libbam-dev
+ libboost-date-time1.46-dev libboost-date-time1.46.1 libboost-dev
libboost-serialization1.46-dev libboost-serialization1.46.1
libboost-thread-dev libboost-thread1.46-dev libboost-thread1.46.1
libboost1.46-dev libcroco3 libexpat1 libffi5 libglib2.0-0 libicu48 libmagic1
libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libtool
libunistring0 libxml2 m4 man-db mime-support po-debconf python
- python-minimal python2.7 python2.7-minimal quilt
+ python-minimal python2.7 python2.7-minimal
sbuild-build-depends-cufflinks-dummy zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/35.9 MB of archives.
-After this operation, 139 MB of additional disk space will be used.
+0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/35.6 MB of archives.
+After this operation, 138 MB of additional disk space will be used.
Selecting previously unselected package libncursesw5.
-(Reading database ... 10811 files and directories currently installed.)
+(Reading database ... 10804 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_amd64.deb) ...
Selecting previously unselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ...
@@ -134,7 +133,7 @@ Unpacking libffi5 (from .../libffi5_3.0.10-3_amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ...
Selecting previously unselected package libexpat1.
@@ -154,15 +153,15 @@ Unpacking file (from .../archives/file_5.09-2_amd64.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ...
Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_amd64.deb) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-3_amd64.deb) ...
Selecting previously unselected package m4.
Unpacking m4 (from .../archives/m4_1.4.16-2_amd64.deb) ...
Selecting previously unselected package mime-support.
Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-8_amd64.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_amd64.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-8_amd64.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.2-9_amd64.deb) ...
Selecting previously unselected package python-minimal.
Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
Selecting previously unselected package python.
@@ -180,39 +179,35 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_amd64.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.12_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package libtool.
Unpacking libtool (from .../libtool_2.4.2-1_amd64.deb) ...
Selecting previously unselected package dh-autoreconf.
Unpacking dh-autoreconf (from .../dh-autoreconf_5_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ...
Selecting previously unselected package libbam-dev.
Unpacking libbam-dev (from .../libbam-dev_0.1.18-1_amd64.deb) ...
Selecting previously unselected package libicu48.
-Unpacking libicu48 (from .../libicu48_4.8.1.1-1_amd64.deb) ...
+Unpacking libicu48 (from .../libicu48_4.8.1.1-2_amd64.deb) ...
Selecting previously unselected package libboost1.46-dev.
-Unpacking libboost1.46-dev (from .../libboost1.46-dev_1.46.1-7+b1_amd64.deb) ...
+Unpacking libboost1.46-dev (from .../libboost1.46-dev_1.46.1-8_amd64.deb) ...
Selecting previously unselected package libboost-date-time1.46.1.
-Unpacking libboost-date-time1.46.1 (from .../libboost-date-time1.46.1_1.46.1-7+b1_amd64.deb) ...
+Unpacking libboost-date-time1.46.1 (from .../libboost-date-time1.46.1_1.46.1-8_amd64.deb) ...
Selecting previously unselected package libboost-serialization1.46.1.
-Unpacking libboost-serialization1.46.1 (from .../libboost-serialization1.46.1_1.46.1-7+b1_amd64.deb) ...
+Unpacking libboost-serialization1.46.1 (from .../libboost-serialization1.46.1_1.46.1-8_amd64.deb) ...
Selecting previously unselected package libboost-serialization1.46-dev.
-Unpacking libboost-serialization1.46-dev (from .../libboost-serialization1.46-dev_1.46.1-7+b1_amd64.deb) ...
+Unpacking libboost-serialization1.46-dev (from .../libboost-serialization1.46-dev_1.46.1-8_amd64.deb) ...
Selecting previously unselected package libboost-date-time1.46-dev.
-Unpacking libboost-date-time1.46-dev (from .../libboost-date-time1.46-dev_1.46.1-7+b1_amd64.deb) ...
+Unpacking libboost-date-time1.46-dev (from .../libboost-date-time1.46-dev_1.46.1-8_amd64.deb) ...
Selecting previously unselected package libboost-dev.
-Unpacking libboost-dev (from .../libboost-dev_1.46.1.1_amd64.deb) ...
+Unpacking libboost-dev (from .../libboost-dev_1.48.0.2_amd64.deb) ...
Selecting previously unselected package libboost-thread1.46.1.
-Unpacking libboost-thread1.46.1 (from .../libboost-thread1.46.1_1.46.1-7+b1_amd64.deb) ...
+Unpacking libboost-thread1.46.1 (from .../libboost-thread1.46.1_1.46.1-8_amd64.deb) ...
Selecting previously unselected package libboost-thread1.46-dev.
-Unpacking libboost-thread1.46-dev (from .../libboost-thread1.46-dev_1.46.1-7+b1_amd64.deb) ...
+Unpacking libboost-thread1.46-dev (from .../libboost-thread1.46-dev_1.46.1-8_amd64.deb) ...
Selecting previously unselected package libboost-thread-dev.
-Unpacking libboost-thread-dev (from .../libboost-thread-dev_1.46.1.1_amd64.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking libboost-thread-dev (from .../libboost-thread-dev_1.48.0.2_amd64.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously unselected package sbuild-build-depends-cufflinks-dummy.
@@ -224,7 +219,7 @@ Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
@@ -237,12 +232,12 @@ Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up libsqlite3-0 (3.7.9-3) ...
Setting up m4 (1.4.16-2) ...
Setting up mime-support (3.51-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-8) ...
-Setting up python2.7 (2.7.2-8) ...
+Setting up python2.7-minimal (2.7.2-9) ...
+Setting up python2.7 (2.7.2-9) ...
Setting up python-minimal (2.7.2-9) ...
Setting up python (2.7.2-9) ...
Setting up autoconf (2.68-1) ...
@@ -252,23 +247,21 @@ update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.12) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
Setting up libtool (2.4.2-1) ...
Setting up dh-autoreconf (5) ...
-Setting up diffstat (1.54-1) ...
Setting up libbam-dev (0.1.18-1) ...
-Setting up libicu48 (4.8.1.1-1) ...
-Setting up libboost1.46-dev (1.46.1-7+b1) ...
-Setting up libboost-date-time1.46.1 (1.46.1-7+b1) ...
-Setting up libboost-serialization1.46.1 (1.46.1-7+b1) ...
-Setting up libboost-serialization1.46-dev (1.46.1-7+b1) ...
-Setting up libboost-date-time1.46-dev (1.46.1-7+b1) ...
-Setting up libboost-dev (1.46.1.1) ...
-Setting up libboost-thread1.46.1 (1.46.1-7+b1) ...
-Setting up libboost-thread1.46-dev (1.46.1-7+b1) ...
-Setting up libboost-thread-dev (1.46.1.1) ...
-Setting up quilt (0.48-8) ...
+Setting up libicu48 (4.8.1.1-2) ...
+Setting up libboost1.46-dev (1.46.1-8) ...
+Setting up libboost-date-time1.46.1 (1.46.1-8) ...
+Setting up libboost-serialization1.46.1 (1.46.1-8) ...
+Setting up libboost-serialization1.46-dev (1.46.1-8) ...
+Setting up libboost-date-time1.46-dev (1.46.1-8) ...
+Setting up libboost-dev (1.48.0.2) ...
+Setting up libboost-thread1.46.1 (1.46.1-8) ...
+Setting up libboost-thread1.46-dev (1.46.1-8) ...
+Setting up libboost-thread-dev (1.48.0.2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up sbuild-build-depends-cufflinks-dummy (0.invalid.0) ...
@@ -277,8 +270,8 @@ Setting up sbuild-build-depends-cufflinks-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-6 gcc-4.6_4.6.2-6 libc6-dev_2.13-21 libstdc++6_4.6.2-6 libstdc++6-4.6-dev_4.6.2-6 linux-libc-dev_3.1.4-1
-Package versions: apt_0.8.15.9 autoconf_2.68-1 automake_1:1.11.1-1 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1 build-essential_11.5 bzip2_1.0.6-1 coreutils_8.13-3 cpp_4:4.6.2-1 cpp-4.6_4.6.2-6 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.12 debian-archive-keyring_2010.08.28 debianutils_4.1 dh-autoreconf_5 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.2-1 g++-4.6_4.6.2-6 gcc_4:4.6.2-1 gcc-4.6_4.6.2-6 gcc-4.6-base_4.6.2-6 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libbam-dev_0.1.18-1 libblkid1_2.20.1-1 libboost-date-time1.46-dev_1.46.1-7+b1 libboost-date-time1.46.1_1.46.1-7+b1 libboost-dev_1.46.1.1 libboost-serialization1.46-dev_1.46.1-7+b1 libboost-serialization1.46.1_1.46.1-7+b1 libboost-thread-dev_1.46.1.1 libboost-thread1.46-dev_1.46.1-7+b1 libboost-thread1.46.1_1.46.1-7+b1 libboost1.46-dev_1.46.1-7+b1 libbz2-1.0_1.0.6-1 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.7_4.7.25-20 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-6 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgmp3c2_2:4.3.2+dfsg-2 libgomp1_4.6.2-6 libicu48_4.8.1.1-1 liblocale-gettext-perl_1.05-7+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-6 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-6 libstdc++6-4.6-dev_4.6.2-6 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtool_2.4.2-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.20.1-1 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.4-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 m4_1.4.16-2 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.20.1-1 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu1 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-8 python2.7-minimal_2.7.2-8 quilt_0.48-8 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-cufflinks-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.20.1-1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-3 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.6-1
+Package versions: apt_0.8.15.9 autoconf_2.68-1 automake_1:1.11.1-1 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1 build-essential_11.5 bzip2_1.0.6-1 coreutils_8.13-3 cpp_4:4.6.2-3 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 dh-autoreconf_5 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-3 g++_4:4.6.2-3 g++-4.6_4.6.2-11 gcc_4:4.6.2-3 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libbam-dev_0.1.18-1 libblkid1_2.20.1-1 libboost-date-time1.46-dev_1.46.1-8 libboost-date-time1.46.1_1.46.1-8 libboost-dev_1.48.0.2 libboost-serialization1.46-dev_1.46.1-8 libboost-serialization1.46.1_1.46.1-8 libboost-thread-dev_1.48.0.2 libboost-thread1.46-dev_1.46.1-8 libboost-thread1.46.1_1.46.1-8 libboost1.46-dev_1.46.1-8 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.7_4.7.25-20 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgmp3c2_2:4.3.2+dfsg-2 libgomp1_4.6.2-11 libicu48_4.8.1.1-2 liblocale-gettext-perl_1.05-7+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-11 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-3 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtool_2.4.2-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.6-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 m4_1.4.16-2 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.20.1-1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-minimal_2.7.2-9 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-cufflinks-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -289,12 +282,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 11 03:38:16 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jan 6 00:21:05 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./cufflinks_1.2.1-1.dsc
-dpkg-source: info: extracting cufflinks in cufflinks-1.2.1
-dpkg-source: info: unpacking cufflinks_1.2.1.orig.tar.gz
-dpkg-source: info: unpacking cufflinks_1.2.1-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./cufflinks_1.3.0-1.dsc
+dpkg-source: info: extracting cufflinks in cufflinks-1.3.0
+dpkg-source: info: unpacking cufflinks_1.3.0.orig.tar.gz
+dpkg-source: info: unpacking cufflinks_1.3.0-1.debian.tar.gz
dpkg-source: info: applying 0001-fix_spelling.patch
dpkg-source: info: applying 0002-bam2samtools.patch
dpkg-source: info: applying 0003-fix_includes_path.patch
@@ -314,7 +307,7 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-d2d85a4d-0eaa-49e5-835c-7d630fe7c990
+SCHROOT_SESSION_ID=sid-amd64-sbuild-48ef29fa-8362-4a84-aa4d-3f35ec1f65b0
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -326,46 +319,25 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package cufflinks
-dpkg-buildpackage: source version 1.2.1-1
+dpkg-buildpackage: source version 1.3.0-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build cufflinks-1.2.1
+ dpkg-source --before-build cufflinks-1.3.0
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory `/«PKGBUILDDIR»'
-dh_quilt_patch
-File series fully applied, ends at patch 0003-fix_includes_path.patch
dh_auto_clean
rm -rf autom4te.cache
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_autoreconf_clean
- debian/rules override_dh_clean
-make[1]: Entering directory `/«PKGBUILDDIR»'
-dh_quilt_unpatch
-Removing patch 0003-fix_includes_path.patch
-Restoring src/hits.h
-
-Removing patch 0002-bam2samtools.patch
-Restoring ax_bam.m4
-
-Removing patch 0001-fix_spelling.patch
-Restoring src/locfit/arith.c
-Restoring src/locfit/lfd.c
-
-No patches applied
-dh_clean
-make[1]: Leaving directory `/«PKGBUILDDIR»'
- dpkg-source -b cufflinks-1.2.1
+ dh_clean
+ dpkg-source -b cufflinks-1.3.0
dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: patches are not applied, applying them now
-dpkg-source: info: applying 0001-fix_spelling.patch
-dpkg-source: info: applying 0002-bam2samtools.patch
-dpkg-source: info: applying 0003-fix_includes_path.patch
-dpkg-source: info: building cufflinks using existing ./cufflinks_1.2.1.orig.tar.gz
-dpkg-source: info: building cufflinks in cufflinks_1.2.1-1.debian.tar.gz
-dpkg-source: info: building cufflinks in cufflinks_1.2.1-1.dsc
+dpkg-source: info: building cufflinks using existing ./cufflinks_1.3.0.orig.tar.gz
+dpkg-source: info: building cufflinks in cufflinks_1.3.0-1.debian.tar.gz
+dpkg-source: info: building cufflinks in cufflinks_1.3.0-1.dsc
debian/rules build
dh build --with autoreconf
dh_testdir
@@ -501,9 +473,9 @@ config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
--- cufflinks 1.2.1 Configuration Results --
+-- cufflinks 1.3.0 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include
- GCC version: gcc (Debian 4.6.2-6) 4.6.2
+ GCC version: gcc (Debian 4.6.2-11) 4.6.2
Host System type: x86_64-pc-linux-gnu
Install prefix: /usr
Install eprefix: ${prefix}
@@ -548,9 +520,9 @@ In file included from differential.h:29:0,
replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable]
differential.cpp: In member function 'void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >&)':
-differential.cpp:111:31: warning: unused variable 's2' [-Wunused-variable]
+differential.cpp:112:31: warning: unused variable 's2' [-Wunused-variable]
differential.cpp: In function 'void sample_abundance_worker(const string&, SampleAbundances&, HitBundle*, bool, bool)':
-differential.cpp:704:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+differential.cpp:1073:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp
In file included from replicates.h:10:0,
from common.cpp:28:
@@ -598,41 +570,41 @@ replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable]
abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&, const boost::numeric::ublas::matrix<double>&, const boost::numeric::ublas::matrix<double>&, const boost::numeric::ublas::matrix<double>&, const boost::numeric::ublas::matrix<double>&, const boost::numeric::ublas::matrix<double>&, long double, const std::set<boost::shared_ptr<const ReadGroupProperties> >&)':
abundances.h:448:27: warning: 'AbundanceGroup::_iterated_exp_count_covariance' will be initialized after [-Wreorder]
abundances.h:443:27: warning: 'boost::numeric::ublas::matrix<double> AbundanceGroup::_count_covariance' [-Wreorder]
-abundances.cpp:375:1: warning: when initialized here [-Wreorder]
+abundances.cpp:74:1: warning: when initialized here [-Wreorder]
abundances.cpp: In member function 'virtual AbundanceStatus AbundanceGroup::status() const':
-abundances.cpp:442:10: warning: variable 'has_lowdata_member' set but not used [-Wunused-but-set-variable]
-abundances.cpp:472:12: warning: variable 'total_gamma' set but not used [-Wunused-but-set-variable]
+abundances.cpp:141:10: warning: variable 'has_lowdata_member' set but not used [-Wunused-but-set-variable]
+abundances.cpp:171:12: warning: variable 'total_gamma' set but not used [-Wunused-but-set-variable]
abundances.cpp: In function 'void collapse_equivalent_hits(const std::vector<MateHit>&, std::vector<boost::shared_ptr<Abundance> >&, std::vector<boost::shared_ptr<Abundance> >&, std::vector<MateHit>&, std::vector<double>&, bool)':
-abundances.cpp:908:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+abundances.cpp:607:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
abundances.cpp: In function 'bool estimate_count_variance(long double&, double, double, double, double, double, double)':
-abundances.cpp:1330:17: warning: variable 'bnb_mean' set but not used [-Wunused-but-set-variable]
+abundances.cpp:1029:17: warning: variable 'bnb_mean' set but not used [-Wunused-but-set-variable]
abundances.cpp: In member function 'bool AbundanceGroup::calculate_gammas(const std::vector<MateHit>&, const std::vector<double>&, const std::vector<boost::shared_ptr<Abundance> >&, const std::vector<boost::shared_ptr<Abundance> >&)':
-abundances.cpp:2140:16: warning: unused variable 'cross_replicate_js' [-Wunused-variable]
+abundances.cpp:1839:16: warning: unused variable 'cross_replicate_js' [-Wunused-variable]
abundances.cpp: In member function 'void AbundanceGroup::calculate_iterated_exp_count_covariance(const std::vector<MateHit>&, const std::vector<boost::shared_ptr<Abundance> >&)':
-abundances.cpp:2320:12: warning: unused variable 'num_salient_frags' [-Wunused-variable]
+abundances.cpp:2019:12: warning: unused variable 'num_salient_frags' [-Wunused-variable]
abundances.cpp: In member function 'void AbundanceGroup::calculate_kappas()':
-abundances.cpp:2437:20: warning: unused variable 'kappa' [-Wunused-variable]
-abundances.cpp:2463:24: warning: unused variable 'den' [-Wunused-variable]
-abundances.cpp:2464:24: warning: unused variable 'counts' [-Wunused-variable]
-abundances.cpp:2466:24: warning: unused variable 'count_var' [-Wunused-variable]
-abundances.cpp:2467:24: warning: unused variable 'kappa' [-Wunused-variable]
+abundances.cpp:2136:20: warning: unused variable 'kappa' [-Wunused-variable]
+abundances.cpp:2162:24: warning: unused variable 'den' [-Wunused-variable]
+abundances.cpp:2163:24: warning: unused variable 'counts' [-Wunused-variable]
+abundances.cpp:2165:24: warning: unused variable 'count_var' [-Wunused-variable]
+abundances.cpp:2166:24: warning: unused variable 'kappa' [-Wunused-variable]
abundances.cpp: In function 'void grad_ascent_step(int, int, const std::vector<double>&, std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<double>&, std::vector<double>&, double&)':
-abundances.cpp:2636:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-abundances.cpp:2639:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-abundances.cpp:2644:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-abundances.cpp:2653:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+abundances.cpp:2335:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+abundances.cpp:2338:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+abundances.cpp:2343:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+abundances.cpp:2352:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
abundances.cpp: In function 'AbundanceStatus bootstrap_gamma_mle(const std::vector<boost::shared_ptr<Abundance> >&, const std::vector<MateHit>&, const std::vector<double>&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&, boost::numeric::ublas::matrix<double>&, double&)':
-abundances.cpp:3359:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-abundances.cpp:3362:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-abundances.cpp:3376:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+abundances.cpp:3058:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+abundances.cpp:3061:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+abundances.cpp:3075:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
abundances.cpp: In function 'AbundanceStatus gamma_mle(const std::vector<boost::shared_ptr<Abundance> >&, const std::vector<MateHit>&, const std::vector<double>&, std::vector<double>&, bool, std::vector<double>*)':
-abundances.cpp:3801:10: warning: variable 'logL' set but not used [-Wunused-but-set-variable]
+abundances.cpp:3500:10: warning: variable 'logL' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o scaffolds.o scaffolds.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o hits.o hits.cpp
hits.cpp: In member function 'void ReadHit::trim(int)':
hits.cpp:38:9: warning: variable 'new_left' set but not used [-Wunused-but-set-variable]
hits.cpp: In member function 'virtual bool BAMHitFactory::inspect_header()':
-hits.cpp:755:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+hits.cpp:760:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o genes.o genes.cpp
In file included from abundances.h:22:0,
from genes.h:18,
@@ -686,16 +658,18 @@ abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<b
abundances.h:448:27: warning: 'AbundanceGroup::_iterated_exp_count_covariance' will be initialized after [-Wreorder]
abundances.h:443:27: warning: 'boost::numeric::ublas::matrix<double> AbundanceGroup::_count_covariance' [-Wreorder]
abundances.h:302:2: warning: when initialized here [-Wreorder]
+filters.cpp: In function 'void pre_mrna_filter(int, int, std::vector<Scaffold>&)':
+filters.cpp:218:11: warning: unused variable 'min_flt_fraction' [-Wunused-variable]
filters.cpp: In function 'void clip_by_3_prime_dropoff(std::vector<Scaffold>&)':
-filters.cpp:820:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-filters.cpp:822:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-filters.cpp:869:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-filters.cpp:795:20: warning: variable 'mean_to_keep' set but not used [-Wunused-but-set-variable]
-filters.cpp:796:20: warning: variable 'mean_to_trim' set but not used [-Wunused-but-set-variable]
-filters.cpp:922:20: warning: unused variable 'avg_cov' [-Wunused-variable]
-filters.cpp:926:36: warning: variable 'exon_3' set but not used [-Wunused-but-set-variable]
-filters.cpp:927:17: warning: variable 'mult' set but not used [-Wunused-but-set-variable]
-filters.cpp:928:17: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
+filters.cpp:834:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+filters.cpp:836:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+filters.cpp:883:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+filters.cpp:809:20: warning: variable 'mean_to_keep' set but not used [-Wunused-but-set-variable]
+filters.cpp:810:20: warning: variable 'mean_to_trim' set but not used [-Wunused-but-set-variable]
+filters.cpp:936:20: warning: unused variable 'avg_cov' [-Wunused-variable]
+filters.cpp:940:36: warning: variable 'exon_3' set but not used [-Wunused-but-set-variable]
+filters.cpp:941:17: warning: variable 'mult' set but not used [-Wunused-but-set-variable]
+filters.cpp:942:17: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o scaffold_graph.o scaffold_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o matching_merge.o matching_merge.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o graph_optimize.o graph_optimize.cpp
@@ -726,6 +700,7 @@ abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<b
abundances.h:448:27: warning: 'AbundanceGroup::_iterated_exp_count_covariance' will be initialized after [-Wreorder]
abundances.h:443:27: warning: 'boost::numeric::ublas::matrix<double> AbundanceGroup::_count_covariance' [-Wreorder]
abundances.h:302:2: warning: when initialized here [-Wreorder]
+g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o sampling.o sampling.cpp
gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o adap.o `test -f 'locfit/adap.c' || echo './'`locfit/adap.c
locfit/adap.c: In function 'mmse':
locfit/adap.c:29:17: warning: variable 'p' set but not used [-Wunused-but-set-variable]
@@ -863,7 +838,7 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasi
jensen_shannon.cpp: In function 'void jensen_shannon_gradient(std::vector<boost::numeric::ublas::vector<double> >&, double, boost::numeric::ublas::vector<double>&)':
jensen_shannon.cpp:230:24: warning: unused variable 'curr_grad' [-Wunused-variable]
rm -f libcufflinks.a
-ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o
+ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o sampling.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o
ranlib libcufflinks.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o codons.o codons.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o GArgs.o GArgs.cpp
@@ -903,20 +878,20 @@ abundances.h:448:27: warning: 'AbundanceGroup::_iterated_exp_count_covariance' w
abundances.h:443:27: warning: 'boost::numeric::ublas::matrix<double> AbundanceGroup::_count_covariance' [-Wreorder]
abundances.h:302:2: warning: when initialized here [-Wreorder]
cufflinks.cpp: In function 'bool scaffolds_for_bundle(const HitBundle&, std::vector<boost::shared_ptr<Scaffold> >&, std::vector<boost::shared_ptr<Scaffold> >*, BundleStats*)':
-cufflinks.cpp:629:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+cufflinks.cpp:630:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cufflinks.cpp: In function 'void quantitate_transcript_cluster(AbundanceGroup&, double, std::vector<Gene>&, bool)':
-cufflinks.cpp:920:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-cufflinks.cpp:928:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+cufflinks.cpp:921:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+cufflinks.cpp:929:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cufflinks.cpp: In function 'void assemble_bundle(const RefSequenceTable&, HitBundle*, BiasLearner*, long double, FILE*, FILE*, FILE*, FILE*)':
-cufflinks.cpp:1200:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+cufflinks.cpp:1201:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cufflinks.cpp: In function 'bool assemble_hits(BundleFactory&, BiasLearner*)':
-cufflinks.cpp:1425:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+cufflinks.cpp:1426:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cufflinks.cpp: In function 'void assemble_bundle(const RefSequenceTable&, HitBundle*, BiasLearner*, long double, FILE*, FILE*, FILE*, FILE*)':
-cufflinks.cpp:1303:28: warning: 'status' may be used uninitialized in this function [-Wuninitialized]
+cufflinks.cpp:1304:28: warning: 'status' may be used uninitialized in this function [-Wuninitialized]
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -L/usr/lib -o cufflinks cufflinks.o libcufflinks.a libgc.a -lboost_thread-mt -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o cuffcompare.o cuffcompare.cpp
cuffcompare.cpp: In function 'void printITrack(FILE*, GList<GffObj>&, int, int&)':
-cuffcompare.cpp:1845:12: warning: variable 'eqref' set but not used [-Wunused-but-set-variable]
+cuffcompare.cpp:1848:12: warning: variable 'eqref' set but not used [-Wunused-but-set-variable]
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -o cuffcompare cuffcompare.o libgc.a -lz
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -c -o cuffdiff.o cuffdiff.cpp
In file included from cuffdiff.cpp:27:0:
@@ -977,8 +952,8 @@ make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
fakeroot debian/rules binary
+make[1]: Leaving directory `/«PKGBUILDDIR»'
dh binary --with autoreconf
dh_testroot
dh_prep
@@ -1044,20 +1019,14 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
debian/rules override_dh_builddeb
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_builddeb -- -Z xz
-dpkg-deb: building package `cufflinks' in `../cufflinks_1.2.1-1_amd64.deb'.
+dpkg-deb: building package `cufflinks' in `../cufflinks_1.3.0-1_amd64.deb'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
- dpkg-genchanges -v0 >../cufflinks_1.2.1-1_amd64.changes
-parsechangelog/debian: warning: 'since' option specifies non-existing version
-parsechangelog/debian: warning: use newest entry that is earlier than the one specified
-parsechangelog/debian: warning: none found, starting from the oldest entry
+ dpkg-genchanges >../cufflinks_1.3.0-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build cufflinks-1.2.1
-dpkg-source: info: unapplying 0003-fix_includes_path.patch
-dpkg-source: info: unapplying 0002-bam2samtools.patch
-dpkg-source: info: unapplying 0001-fix_spelling.patch
+ dpkg-source --after-build cufflinks-1.3.0
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111211-1246
+Build finished at 20120106-0929
Finished
────────
@@ -1069,99 +1038,64 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-cufflinks_1.2.1-1_amd64.changes:
+cufflinks_1.3.0-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Sun, 11 Dec 2011 12:07:02 +0900
+Date: Fri, 06 Jan 2012 09:20:23 +0900
Source: cufflinks
Binary: cufflinks
Architecture: source amd64
-Version: 1.2.1-1
+Version: 1.3.0-1
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:
cufflinks - Transcript assembly, differential expression and regulation for R
-Closes: 627799
Changes:
- cufflinks (1.2.1-1) unstable; urgency=low
+ cufflinks (1.3.0-1) unstable; urgency=low
.
[ Alexandre Mestiashvili ]
* New upstream release
- * added patch to fix bam.h location .
- * debian/rules invoke autoreconf
- * debian/rules added overrides for dh_auto_clean and dh_clean
- * added missing dependency - quilt .We use dh_quilt_patch,
- dh_quilt_unpatch helpers
- * debian/control added dependency python (>=2.6.6-3~) for source package
- * debian/control added dependency python (>=2.6.6-3~) for binary package
- .
- [ Andreas Tille ]
- * Added myself to uploaders
- * Debhelper 8 (control+compat)
- * debian/watch: removed dh-make template from watch file
- * debian/rules: invoke autotools_dev
+ * Fixed spelling error.
+ * Updated source version
.
[ Charles Plessy ]
- * Switch to non-free section because of the locfit license (debian/control).
- * Added myself to Uploaders (debian/control).
- * Compress binary package with xz (debian/rules).
- * Pre-depend on dpkg (>= 1.15.6) for xz compression (Ubuntu LTS).
- .
- cufflinks (1.0.3-1) UNRELEASED; urgency=low
- .
- [ Alex Mestiashvili ]
- * added docs
- * added missing dependency
- * libbam-dev provides necessary headers only from 0.1.16 version .
- Fixed in control file.
- .
- [ Charles Plessy ]
- * Add debian/gbp.conf to show the package is managed with git-buildpackage.
- * Converted Debian copyright file to machine-readable format (DEP 5).
- * Reviewed copyright and license notices, and found that locfit is non-free…
- .
- [ Alex Mestiashvili ]
- * Imported Upstream version 1.0.3 (bugfix)
- .
- cufflinks (1.0.2-1) UNRELEASED; urgency=low
- .
- * Initial release (Closes: #627799)
+ * Removed quilt patch management, and rely on dpkg-dev exclusively.
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Checksums-Sha256:
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Files:
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+ 145ebe5e6a1e3a6ea0160369fc933853 1295 non-free/science optional cufflinks_1.3.0-1.dsc
+ 6914059cf8c8f22eb388e1fde44deabe 676660 non-free/science optional cufflinks_1.3.0.orig.tar.gz
+ 44296465461c9626c80056250d8bb018 11608 non-free/science optional cufflinks_1.3.0-1.debian.tar.gz
+ 813ba638f1fd5e842db198967f3a196e 1003092 non-free/science optional cufflinks_1.3.0-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-cufflinks_1.2.1-1_amd64.deb
+cufflinks_1.3.0-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 1002762 bytes: control archive= 1194 bytes.
+ size 1003092 bytes: control archive= 1199 bytes.
870 bytes, 16 lines control
1123 bytes, 18 lines md5sums
Package: cufflinks
- Version: 1.2.1-1
+ Version: 1.3.0-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5577
+ Installed-Size: 5582
Pre-Depends: dpkg (>= 1.15.6)
Depends: libboost-thread1.46.1 (>= 1.46.1-1), libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.3.3.dfsg), python (>= 2.6.6-3~)
Section: non-free/science
@@ -1174,32 +1108,32 @@ cufflinks_1.2.1-1_amd64.deb
transcripts. Cufflinks then estimates the relative abundances of these
transcripts based on how many reads support each one.
-drwxr-xr-x root/root 0 2011-12-11 12:46 ./
-drwxr-xr-x root/root 0 2011-12-11 12:46 ./usr/
-drwxr-xr-x root/root 0 2011-12-11 12:46 ./usr/share/
-drwxr-xr-x root/root 0 2011-12-11 12:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-12-11 12:46 ./usr/share/doc/cufflinks/
+drwxr-xr-x root/root 0 2012-01-06 09:29 ./
+drwxr-xr-x root/root 0 2012-01-06 09:29 ./usr/
+drwxr-xr-x root/root 0 2012-01-06 09:29 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-06 09:29 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-06 09:29 ./usr/share/doc/cufflinks/
-rw-r--r-- root/root 3536 2011-06-03 11:19 ./usr/share/doc/cufflinks/README
-rw-r--r-- root/root 779 2011-06-03 11:19 ./usr/share/doc/cufflinks/AUTHORS
--rw-r--r-- root/root 8126 2011-12-11 11:23 ./usr/share/doc/cufflinks/copyright
--rw-r--r-- root/root 866 2011-12-11 12:08 ./usr/share/doc/cufflinks/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-12-11 12:46 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-12-11 12:46 ./usr/share/man/man1/
--rw-r--r-- root/root 658 2011-12-11 12:46 ./usr/share/man/man1/cuffmerge.1.gz
--rw-r--r-- root/root 1143 2011-12-11 12:46 ./usr/share/man/man1/cuffcompare.1.gz
--rw-r--r-- root/root 1718 2011-12-11 12:46 ./usr/share/man/man1/cufflinks.1.gz
--rw-r--r-- root/root 396 2011-12-11 12:46 ./usr/share/man/man1/compress_gtf.1.gz
--rw-r--r-- root/root 1266 2011-12-11 12:46 ./usr/share/man/man1/cuffdiff.1.gz
--rw-r--r-- root/root 339 2011-12-11 12:46 ./usr/share/man/man1/gtf_to_sam.1.gz
--rw-r--r-- root/root 1622 2011-12-11 12:46 ./usr/share/man/man1/gffread.1.gz
-drwxr-xr-x root/root 0 2011-12-11 12:46 ./usr/bin/
--rwxr-xr-x root/root 1607168 2011-12-11 12:46 ./usr/bin/cufflinks
--rwxr-xr-x root/root 318792 2011-12-11 12:46 ./usr/bin/cuffcompare
--rwxr-xr-x root/root 1003392 2011-12-11 12:46 ./usr/bin/compress_gtf
--rwxr-xr-x root/root 1476032 2011-12-11 12:46 ./usr/bin/cuffdiff
--rwxr-xr-x root/root 996128 2011-12-11 12:46 ./usr/bin/gtf_to_sam
--rwxr-xr-x root/root 232672 2011-12-11 12:46 ./usr/bin/gffread
--rwxr-xr-x root/root 18983 2011-12-11 12:46 ./usr/bin/cuffmerge
+-rw-r--r-- root/root 8126 2012-01-06 08:30 ./usr/share/doc/cufflinks/copyright
+-rw-r--r-- root/root 952 2012-01-06 09:20 ./usr/share/doc/cufflinks/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-01-06 09:29 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-01-06 09:29 ./usr/share/man/man1/
+-rw-r--r-- root/root 658 2012-01-06 09:29 ./usr/share/man/man1/cuffmerge.1.gz
+-rw-r--r-- root/root 1143 2012-01-06 09:29 ./usr/share/man/man1/cuffcompare.1.gz
+-rw-r--r-- root/root 1718 2012-01-06 09:29 ./usr/share/man/man1/cufflinks.1.gz
+-rw-r--r-- root/root 396 2012-01-06 09:29 ./usr/share/man/man1/compress_gtf.1.gz
+-rw-r--r-- root/root 1266 2012-01-06 09:29 ./usr/share/man/man1/cuffdiff.1.gz
+-rw-r--r-- root/root 339 2012-01-06 09:29 ./usr/share/man/man1/gtf_to_sam.1.gz
+-rw-r--r-- root/root 1622 2012-01-06 09:29 ./usr/share/man/man1/gffread.1.gz
+drwxr-xr-x root/root 0 2012-01-06 09:29 ./usr/bin/
+-rwxr-xr-x root/root 1611296 2012-01-06 09:29 ./usr/bin/cufflinks
+-rwxr-xr-x root/root 318792 2012-01-06 09:29 ./usr/bin/cuffcompare
+-rwxr-xr-x root/root 999648 2012-01-06 09:29 ./usr/bin/compress_gtf
+-rwxr-xr-x root/root 1484224 2012-01-06 09:29 ./usr/bin/cuffdiff
+-rwxr-xr-x root/root 992672 2012-01-06 09:29 ./usr/bin/gtf_to_sam
+-rwxr-xr-x root/root 232672 2012-01-06 09:29 ./usr/bin/gffread
+-rwxr-xr-x root/root 19134 2012-01-06 09:29 ./usr/bin/cuffmerge
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1210,12 +1144,9 @@ drwxr-xr-x root/root 0 2011-12-11 12:46 ./usr/bin/
lintian
───────
-P: cufflinks source: unneeded-build-dep-on-quilt
P: cufflinks source: unversioned-copyright-format-uri http://dep.debian.net/deps/dep5
I: cufflinks: spelling-error-in-binary usr/bin/compress_gtf ang and
-I: cufflinks: spelling-error-in-binary usr/bin/cuffdiff intial initial
I: cufflinks: spelling-error-in-binary usr/bin/cuffdiff ang and
-I: cufflinks: spelling-error-in-binary usr/bin/cufflinks intial initial
I: cufflinks: spelling-error-in-binary usr/bin/cufflinks ang and
I: cufflinks: spelling-error-in-binary usr/bin/gtf_to_sam ang and
P: cufflinks: no-upstream-changelog
@@ -1236,19 +1167,19 @@ Building dependency tree...
Reading state information...
The following packages will be REMOVED:
autoconf* automake* autotools-dev* bsdmainutils* debhelper* dh-autoreconf*
- diffstat* file* gettext* gettext-base* groff-base* html2text*
- intltool-debian* libbam-dev* libboost-date-time1.46-dev*
- libboost-date-time1.46.1* libboost-dev* libboost-serialization1.46-dev*
- libboost-serialization1.46.1* libboost-thread-dev* libboost-thread1.46-dev*
- libboost-thread1.46.1* libboost1.46-dev* libcroco3* libexpat1* libffi5*
- libglib2.0-0* libicu48* libmagic1* libncursesw5* libpcre3* libpipeline1*
- libsqlite3-0* libssl1.0.0* libtool* libunistring0* libxml2* m4* man-db*
- mime-support* po-debconf* python* python-minimal* python2.7*
- python2.7-minimal* quilt* sbuild-build-depends-core-dummy*
- sbuild-build-depends-cufflinks-dummy* zlib1g-dev*
-0 upgraded, 0 newly installed, 49 to remove and 0 not upgraded.
-After this operation, 139 MB disk space will be freed.
-(Reading database ... 22163 files and directories currently installed.)
+ file* gettext* gettext-base* groff-base* html2text* intltool-debian*
+ libbam-dev* libboost-date-time1.46-dev* libboost-date-time1.46.1*
+ libboost-dev* libboost-serialization1.46-dev* libboost-serialization1.46.1*
+ libboost-thread-dev* libboost-thread1.46-dev* libboost-thread1.46.1*
+ libboost1.46-dev* libcroco3* libexpat1* libffi5* libglib2.0-0* libicu48*
+ libmagic1* libncursesw5* libpcre3* libpipeline1* libsqlite3-0* libssl1.0.0*
+ libtool* libunistring0* libxml2* m4* man-db* mime-support* po-debconf*
+ python* python-minimal* python2.7* python2.7-minimal*
+ sbuild-build-depends-core-dummy* sbuild-build-depends-cufflinks-dummy*
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 47 to remove and 0 not upgraded.
+After this operation, 138 MB disk space will be freed.
+(Reading database ... 22070 files and directories currently installed.)
Removing sbuild-build-depends-cufflinks-dummy ...
Removing dh-autoreconf ...
Removing automake ...
@@ -1256,14 +1187,11 @@ Removing autoconf ...
Purging configuration files for autoconf ...
Removing libtool ...
Removing autotools-dev ...
-Removing quilt ...
-Purging configuration files for quilt ...
Removing debhelper ...
Removing man-db ...
Purging configuration files for man-db ...
Removing bsdmainutils ...
Purging configuration files for bsdmainutils ...
-Removing diffstat ...
Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
@@ -1330,18 +1258,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 205776
-Build-Time: 280
+Build-Space: 207816
+Build-Time: 487
Distribution: unstable
-Install-Time: 19
-Job: cufflinks_1.2.1-1.dsc
+Install-Time: 20
+Job: cufflinks_1.3.0-1.dsc
Lintian: pass
Package: cufflinks
-Package-Time: 303
-Source-Version: 1.2.1-1
-Space: 205776
+Package-Time: 513
+Source-Version: 1.3.0-1
+Space: 207816
Status: successful
-Version: 1.2.1-1
+Version: 1.3.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111211-1246
-Build needed 00:05:03, 205776k disc space
+Finished at 20120106-0929
+Build needed 00:08:33, 207816k disc space
diff --git a/upload b/upload
index 3334082..87bb4e0 100644
--- a/upload
+++ b/upload
@@ -1,6 +1,6 @@
-u cufflinks_1.2.1-1.dsc ftp.upload.debian.org Sun Dec 11 12:50:22 2011
-u cufflinks_1.2.1-1.debian.tar.gz ftp.upload.debian.org Sun Dec 11 12:50:24 2011
-u cufflinks_1.2.1-1_amd64.deb ftp.upload.debian.org Sun Dec 11 12:50:27 2011
-u cufflinks_1.2.1.orig.tar.gz ftp.upload.debian.org Sun Dec 11 12:50:30 2011
-u cufflinks_1.2.1-1_amd64.changes ftp.upload.debian.org Sun Dec 11 12:50:31 2011
-s cufflinks_1.2.1-1_amd64.changes ftp.upload.debian.org Sun Dec 11 12:50:31 2011
+u cufflinks_1.3.0-1.dsc ftp.upload.debian.org Fri Jan 6 09:34:52 2012
+u cufflinks_1.3.0-1.debian.tar.gz ftp.upload.debian.org Fri Jan 6 09:34:54 2012
+u cufflinks_1.3.0-1_amd64.deb ftp.upload.debian.org Fri Jan 6 09:34:57 2012
+u cufflinks_1.3.0.orig.tar.gz ftp.upload.debian.org Fri Jan 6 09:35:00 2012
+u cufflinks_1.3.0-1_amd64.changes ftp.upload.debian.org Fri Jan 6 09:35:01 2012
+s cufflinks_1.3.0-1_amd64.changes ftp.upload.debian.org Fri Jan 6 09:35:01 2012
--
Transcript assembly, differential expression, and differential regulation for RNA-Seq.
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