[med-svn] [SCM] cufflinks branch, builds/amd64, updated. builds/amd64/1.3.0-1-1-gcbcfb48
Charles Plessy
plessy at debian.org
Wed May 9 00:02:42 UTC 2012
The following commit has been merged in the builds/amd64 branch:
commit cbcfb480416b4ac4e6fc45b0b2c53dc64433a002
Author: Charles Plessy <plessy at debian.org>
Date: Wed May 9 09:02:16 2012 +0900
Attempted to rebuild, but it fails.
diff --git a/log b/log
index 37155c4..82d67dd 100644
--- a/log
+++ b/log
@@ -1,33 +1,50 @@
-sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on aqwa.igloo
+sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ cufflinks 1.3.0-1 (amd64) 06 janv. 2012 09:21 ║
+║ cufflinks 1.3.0-2 (amd64) 09 mai 2012 08:36 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: cufflinks
-Version: 1.3.0-1
-Source Version: 1.3.0-1
+Version: 1.3.0-2
+Source Version: 1.3.0-2
Distribution: unstable
Architecture: amd64
-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»'
+I: NOTICE: Log filtering will replace 'build/cufflinks-WalK0f/cufflinks-1.3.0' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/cufflinks-WalK0f' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-c0f656a9-be50-4fae-a8c6-6763088b32b6' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Hit ftp://ftp.jaist.ac.jp sid InRelease
-Hit ftp://ftp.jaist.ac.jp sid/main Sources/DiffIndex
-Hit ftp://ftp.jaist.ac.jp sid/main amd64 Packages/DiffIndex
-Hit ftp://ftp.jaist.ac.jp sid/main TranslationIndex
-Hit ftp://ftp.jaist.ac.jp sid/main Translation-fr
+Get:1 ftp://ftp.us.debian.org sid InRelease [225 kB]
+Get:2 ftp://ftp.us.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:3 ftp://ftp.us.debian.org sid/main amd64 Packages/DiffIndex [7876 B]
+Get:4 ftp://ftp.us.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:5 ftp://ftp.us.debian.org sid/main 2012-05-08-2018.17.pdiff [20.5 kB]
+Get:6 ftp://ftp.us.debian.org sid/main 2012-05-08-2018.17.pdiff [20.5 kB]
+Get:7 ftp://ftp.us.debian.org sid/main amd64 2012-05-08-2018.17.pdiff [20.9 kB]
+Get:8 ftp://ftp.us.debian.org sid/main amd64 2012-05-08-2018.17.pdiff [20.9 kB]
+Get:9 ftp://ftp.us.debian.org sid/main 2012-05-08-2018.17.pdiff [1419 B]
+Get:10 ftp://ftp.us.debian.org sid/main 2012-05-08-2018.17.pdiff [1419 B]
+Fetched 292 kB in 15s (19.1 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+The following packages will be upgraded:
+ libgmp10
+1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Need to get 250 kB of archives.
+After this operation, 44.0 kB disk space will be freed.
+Get:1 ftp://ftp.us.debian.org/debian/ sid/main libgmp10 amd64 2:5.0.5+dfsg-1.1 [250 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 250 kB in 3s (67.2 kB/s)
+(Reading database ... 11729 files and directories currently installed.)
+Preparing to replace libgmp10:amd64 2:5.0.5+dfsg-1 (using .../libgmp10_2%3a5.0.5+dfsg-1.1_amd64.deb) ...
+Unpacking replacement libgmp10:amd64 ...
+Setting up libgmp10:amd64 (2:5.0.5+dfsg-1.1) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -37,14 +54,14 @@ Reading state information...
Local sources
─────────────
-cufflinks_1.3.0-1.dsc exists in .; copying to chroot
+cufflinks_1.3.0-2.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-ixoWFD/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-BMLHA3/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -56,6 +73,9 @@ Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
+The following packages were automatically installed and are no longer required:
+ g++-4.6 libstdc++6-4.6-dev
+Use 'apt-get autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
@@ -63,12 +83,12 @@ debconf: delaying package configuration, since apt-utils is not installed
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 ... 10804 files and directories currently installed.)
+(Reading database ... 11729 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, 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'.
+dpkg-deb: building package `sbuild-build-depends-cufflinks-dummy' in `/«BUILDDIR»/resolver-Y1AF0V/apt_archive/sbuild-build-depends-cufflinks-dummy.deb'.
OK
Reading package lists...
@@ -82,196 +102,245 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
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 zlib1g-dev
+ gettext gettext-base groff-base html2text intltool-debian libasprintf0c2
+ libbam-dev libboost-date-time1.49-dev libboost-date-time1.49.0 libboost-dev
+ libboost-serialization1.49-dev libboost-serialization1.49.0
+ libboost-thread-dev libboost-thread1.49-dev libboost-thread1.49.0
+ libboost1.49-dev libcroco3 libexpat1 libffi5 libgettextpo0 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 zlib1g-dev
Suggested packages:
autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist
- whois vacation dh-make gettext-doc groff libboost1.46-doc
- libboost-filesystem1.46-dev libboost-graph-parallel1.46-dev
- libboost-graph1.46-dev libboost-iostreams1.46-dev libboost-math1.46-dev
- libboost-mpi1.46-dev libboost-program-options1.46-dev
- libboost-python1.46-dev libboost-random1.46-dev libboost-regex1.46-dev
- 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
+ whois vacation dh-make gettext-doc groff libboost-doc libboost1.49-doc
+ libboost-chrono1.49-dev libboost-filesystem1.49-dev
+ libboost-graph-parallel1.49-dev libboost-graph1.49-dev
+ libboost-iostreams1.49-dev libboost-locale1.49-dev libboost-math1.49-dev
+ libboost-mpi1.49-dev libboost-program-options1.49-dev
+ libboost-python1.49-dev libboost-random1.49-dev libboost-regex1.49-dev
+ libboost-signals1.49-dev libboost-system1.49-dev libboost-test1.49-dev
+ libboost-timer1.49-dev libboost-wave1.49-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
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 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
+ gettext gettext-base groff-base html2text intltool-debian libasprintf0c2
+ libbam-dev libboost-date-time1.49-dev libboost-date-time1.49.0 libboost-dev
+ libboost-serialization1.49-dev libboost-serialization1.49.0
+ libboost-thread-dev libboost-thread1.49-dev libboost-thread1.49.0
+ libboost1.49-dev libcroco3 libexpat1 libffi5 libgettextpo0 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-cufflinks-dummy zlib1g-dev
+0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
+Need to get 35.7 MB/37.3 MB of archives.
+After this operation, 172 MB of additional disk space will be used.
+Get:1 ftp://ftp.us.debian.org/debian/ sid/main libncursesw5 amd64 5.9-7 [140 kB]
+Get:2 ftp://ftp.us.debian.org/debian/ sid/main libpipeline1 amd64 1.2.1-1 [39.2 kB]
+Get:3 ftp://ftp.us.debian.org/debian/ sid/main libssl1.0.0 amd64 1.0.1b-1 [1210 kB]
+Get:4 ftp://ftp.us.debian.org/debian/ sid/main libasprintf0c2 amd64 0.18.1.1-7 [26.5 kB]
+Get:5 ftp://ftp.us.debian.org/debian/ sid/main libmagic1 amd64 5.11-1 [250 kB]
+Get:6 ftp://ftp.us.debian.org/debian/ sid/main libpcre3 amd64 1:8.30-5 [242 kB]
+Get:7 ftp://ftp.us.debian.org/debian/ sid/main libsqlite3-0 amd64 3.7.11-3 [440 kB]
+Get:8 ftp://ftp.us.debian.org/debian/ sid/main libxml2 amd64 2.7.8.dfsg-9 [895 kB]
+Get:9 ftp://ftp.us.debian.org/debian/ sid/main libglib2.0-0 amd64 2.32.2-1 [2076 kB]
+Get:10 ftp://ftp.us.debian.org/debian/ sid/main libcroco3 amd64 0.6.5-1 [151 kB]
+Get:11 ftp://ftp.us.debian.org/debian/ sid/main libexpat1 amd64 2.1.0-1 [141 kB]
+Get:12 ftp://ftp.us.debian.org/debian/ sid/main libgettextpo0 amd64 0.18.1.1-7 [142 kB]
+Get:13 ftp://ftp.us.debian.org/debian/ sid/main libicu48 amd64 4.8.1.1-6 [8131 kB]
+Get:14 ftp://ftp.us.debian.org/debian/ sid/main bsdmainutils amd64 9.0.1 [210 kB]
+Get:15 ftp://ftp.us.debian.org/debian/ sid/main groff-base amd64 1.21-7 [1151 kB]
+Get:16 ftp://ftp.us.debian.org/debian/ sid/main man-db amd64 2.6.1-2 [1057 kB]
+Get:17 ftp://ftp.us.debian.org/debian/ sid/main file amd64 5.11-1 [53.2 kB]
+Get:18 ftp://ftp.us.debian.org/debian/ sid/main gettext-base amd64 0.18.1.1-7 [152 kB]
+Get:19 ftp://ftp.us.debian.org/debian/ sid/main m4 amd64 1.4.16-3 [260 kB]
+Get:20 ftp://ftp.us.debian.org/debian/ sid/main mime-support all 3.52-1 [35.5 kB]
+Get:21 ftp://ftp.us.debian.org/debian/ sid/main python2.7-minimal amd64 2.7.3~rc2-2.1 [1770 kB]
+Get:22 ftp://ftp.us.debian.org/debian/ sid/main python2.7 amd64 2.7.3~rc2-2.1 [2716 kB]
+Get:23 ftp://ftp.us.debian.org/debian/ sid/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:24 ftp://ftp.us.debian.org/debian/ sid/main python all 2.7.2-10 [177 kB]
+Get:25 ftp://ftp.us.debian.org/debian/ sid/main autoconf all 2.69-1 [589 kB]
+Get:26 ftp://ftp.us.debian.org/debian/ sid/main autotools-dev all 20120210.1 [72.7 kB]
+Get:27 ftp://ftp.us.debian.org/debian/ sid/main automake all 1:1.11.5-1 [606 kB]
+Get:28 ftp://ftp.us.debian.org/debian/ sid/main gettext amd64 0.18.1.1-7 [1966 kB]
+Get:29 ftp://ftp.us.debian.org/debian/ sid/main debhelper all 9.20120419 [694 kB]
+Get:30 ftp://ftp.us.debian.org/debian/ sid/main dh-autoreconf all 6 [15.3 kB]
+Get:31 ftp://ftp.us.debian.org/debian/ sid/main libboost1.49-dev amd64 1.49.0-3 [9266 kB]
+Get:32 ftp://ftp.us.debian.org/debian/ sid/main libboost-date-time1.49.0 amd64 1.49.0-3 [46.1 kB]
+Get:33 ftp://ftp.us.debian.org/debian/ sid/main libboost-serialization1.49.0 amd64 1.49.0-3 [209 kB]
+Get:34 ftp://ftp.us.debian.org/debian/ sid/main libboost-serialization1.49-dev amd64 1.49.0-3 [305 kB]
+Get:35 ftp://ftp.us.debian.org/debian/ sid/main libboost-date-time1.49-dev amd64 1.49.0-3 [49.0 kB]
+Get:36 ftp://ftp.us.debian.org/debian/ sid/main libboost-dev amd64 1.49.0.1 [3022 B]
+Get:37 ftp://ftp.us.debian.org/debian/ sid/main libboost-thread1.49.0 amd64 1.49.0-3 [60.5 kB]
+Get:38 ftp://ftp.us.debian.org/debian/ sid/main libboost-thread1.49-dev amd64 1.49.0-3 [65.7 kB]
+Get:39 ftp://ftp.us.debian.org/debian/ sid/main libboost-thread-dev amd64 1.49.0.1 [2736 B]
+Get:40 ftp://ftp.us.debian.org/debian/ sid/main zlib1g-dev amd64 1:1.2.7.dfsg-1 [214 kB]
debconf: delaying package configuration, since apt-utils is not installed
-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 ... 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) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_amd64.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
-Selecting previously unselected package libffi5.
-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-5.1_amd64.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_amd64.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ...
+Fetched 35.7 MB in 2min 33s (233 kB/s)
+Selecting previously unselected package libncursesw5:amd64.
+(Reading database ... 11729 files and directories currently installed.)
+Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9-7_amd64.deb) ...
+Selecting previously unselected package libpipeline1:amd64.
+Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.1-1_amd64.deb) ...
+Selecting previously unselected package libssl1.0.0:amd64.
+Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1b-1_amd64.deb) ...
+Selecting previously unselected package libasprintf0c2:amd64.
+Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-7_amd64.deb) ...
+Selecting previously unselected package libmagic1:amd64.
+Unpacking libmagic1:amd64 (from .../libmagic1_5.11-1_amd64.deb) ...
+Selecting previously unselected package libpcre3:amd64.
+Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.30-5_amd64.deb) ...
+Selecting previously unselected package libsqlite3-0:amd64.
+Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.11-3_amd64.deb) ...
+Selecting previously unselected package libxml2:amd64.
+Unpacking libxml2:amd64 (from .../libxml2_2.7.8.dfsg-9_amd64.deb) ...
+Selecting previously unselected package libffi5:amd64.
+Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ...
+Selecting previously unselected package libglib2.0-0:amd64.
+Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.32.2-1_amd64.deb) ...
+Selecting previously unselected package libcroco3:amd64.
+Unpacking libcroco3:amd64 (from .../libcroco3_0.6.5-1_amd64.deb) ...
+Selecting previously unselected package libexpat1:amd64.
+Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-1_amd64.deb) ...
+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_0.18.1.1-7_amd64.deb) ...
+Selecting previously unselected package libicu48:amd64.
+Unpacking libicu48:amd64 (from .../libicu48_4.8.1.1-6_amd64.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_amd64.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-7_amd64.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-3_amd64.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-2_amd64.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_amd64.deb) ...
+Unpacking file (from .../archives/file_5.11-1_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_3.7.9-3_amd64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-7_amd64.deb) ...
Selecting previously unselected package m4.
-Unpacking m4 (from .../archives/m4_1.4.16-2_amd64.deb) ...
+Unpacking m4 (from .../archives/m4_1.4.16-3_amd64.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_amd64.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc2-2.1_amd64.deb) ...
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-Unpacking python2.7 (from .../python2.7_2.7.2-9_amd64.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc2-2.1_amd64.deb) ...
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Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
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-Unpacking autotools-dev (from .../autotools-dev_20110511.1_all.deb) ...
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Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
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Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
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Unpacking libtool (from .../libtool_2.4.2-1_amd64.deb) ...
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Unpacking libbam-dev (from .../libbam-dev_0.1.18-1_amd64.deb) ...
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+Unpacking libboost-thread-dev (from .../libboost-thread-dev_1.49.0.1_amd64.deb) ...
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-Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libncursesw5:amd64 (5.9-7) ...
+Setting up libpipeline1:amd64 (1.2.1-1) ...
+Setting up libssl1.0.0:amd64 (1.0.1b-1) ...
+Setting up libasprintf0c2:amd64 (0.18.1.1-7) ...
+Setting up libmagic1:amd64 (5.11-1) ...
+Setting up libpcre3:amd64 (1:8.30-5) ...
+Setting up libsqlite3-0:amd64 (3.7.11-3) ...
+Setting up libxml2:amd64 (2.7.8.dfsg-9) ...
+Setting up libffi5:amd64 (3.0.10-3) ...
+Setting up libglib2.0-0:amd64 (2.32.2-1) ...
No schema files found: doing nothing.
-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) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up libcroco3:amd64 (0.6.5-1) ...
+Setting up libexpat1:amd64 (2.1.0-1) ...
+Setting up libunistring0:amd64 (0.9.3-5) ...
+Setting up libgettextpo0:amd64 (0.18.1.1-7) ...
+Setting up libicu48:amd64 (4.8.1.1-6) ...
+Setting up bsdmainutils (9.0.1) ...
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 (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up groff-base (1.21-7) ...
+Setting up man-db (2.6.1-2) ...
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 (3.7.9-3) ...
-Setting up m4 (1.4.16-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up file (5.11-1) ...
+Setting up gettext-base (0.18.1.1-7) ...
+Setting up m4 (1.4.16-3) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-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) ...
-Setting up autotools-dev (20110511.1) ...
-Setting up automake (1:1.11.1-1) ...
+Setting up python2.7-minimal (2.7.3~rc2-2.1) ...
+Setting up python2.7 (2.7.3~rc2-2.1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up autoconf (2.69-1) ...
+Setting up autotools-dev (20120210.1) ...
+Setting up automake (1:1.11.5-1) ...
update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode.
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-7) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120419) ...
Setting up libtool (2.4.2-1) ...
-Setting up dh-autoreconf (5) ...
+Setting up dh-autoreconf (6) ...
Setting up libbam-dev (0.1.18-1) ...
-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 libboost1.49-dev (1.49.0-3) ...
+Setting up libboost-date-time1.49.0 (1.49.0-3) ...
+Setting up libboost-serialization1.49.0 (1.49.0-3) ...
+Setting up libboost-serialization1.49-dev (1.49.0-3) ...
+Setting up libboost-date-time1.49-dev (1.49.0-3) ...
+Setting up libboost-dev (1.49.0.1) ...
+Setting up libboost-thread1.49.0 (1.49.0-3) ...
+Setting up libboost-thread1.49-dev (1.49.0-3) ...
+Setting up libboost-thread-dev (1.49.0.1) ...
+Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-1) ...
Setting up sbuild-build-depends-cufflinks-dummy (0.invalid.0) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-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
+Kernel: Linux 3.2.0-2-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.3 g++-4.6_4.6.3-5 g++-4.7_4.7.0-7 gcc-4.6_4.6.3-5 gcc-4.7_4.7.0-7 libc6-dev_2.13-32 libstdc++6_4.7.0-7 libstdc++6-4.6-dev_4.6.3-5 libstdc++6-4.7-dev_4.7.0-7 linux-libc-dev_3.2.16-1
+Package versions: apt_0.9.2 autoconf_2.69-1 automake_1:1.11.5-1 autotools-dev_20120210.1 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5 bzip2_1.0.6-1 coreutils_8.13-3.2 cpp_4:4.7.0-6 cpp-4.6_4.6.3-5 cpp-4.7_4.7.0-7 dash_0.5.7-3 debconf_1.5.43 debconf-i18n_1.5.43 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2012.1 debianutils_4.3 dh-autoreconf_6 diffutils_1:3.2-6 dpkg_1.16.3 dpkg-dev_1.16.3 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.7.0-6 g++-4.6_4.6.3-5 g++-4.7_4.7.0-7 gcc_4:4.7.0-6 gcc-4.6_4.6.3-5 gcc-4.6-base_4.6.3-5 gcc-4.7_4.7.0-7 gcc-4.7-base_4.7.0-7 gettext_0.18.1.1-7 gettext-base_0.18.1.1-7 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-1 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libapt-pkg4.12_0.9.2 libasprintf0c2_0.18.1.1-7 libattr1_1:2.4.46-5 libbam-dev_0.1.18-1 libblkid1_2.20.1-4 libboost-date-time1.49-dev_1.49.0-3 libboost-date-time1.49.0_1.49.0-3 libboost-dev_1.49.0.1 libboost-serialization1.49-dev_1.49.0-3 libboost-serialization1.49.0_1.49.0-3 libboost-thread-dev_1.49.0.1 libboost-thread1.49-dev_1.49.0-3 libboost-thread1.49.0_1.49.0-3 libboost1.49-dev_1.49.0-3 libbz2-1.0_1.0.6-1 libc-bin_2.13-32 libc-dev-bin_2.13-32 libc6_2.13-32 libc6-dev_2.13-32 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.3 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-1+b1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-7 libgdbm3_1.8.3-10 libgettextpo0_0.18.1.1-7 libglib2.0-0_2.32.2-1 libgmp10_2:5.0.5+dfsg-1.1 libgmp3c2_2:4.3.2+dfsg-2 libgomp1_4.7.0-7 libicu48_4.8.1.1-6 libitm1_4.7.0-7 liblocale-gettext-perl_1.05-7+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-7 libncursesw5_5.9-7 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libpod-plainer-perl_1.03-1 libquadmath0_4.7.0-7 libreadline6_6.2-8 libselinux1_2.1.9-4 libsemanage-common_2.1.6-5 libsemanage1_2.1.6-5 libsepol1_2.1.4-3 libslang2_2.2.4-10 libsqlite3-0_3.7.11-3 libss2_1.42.2-2 libssl1.0.0_1.0.1b-1 libstdc++6_4.7.0-7 libstdc++6-4.6-dev_4.6.3-5 libstdc++6-4.7-dev_4.7.0-7 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_5.9-7 libtool_2.4.2-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-21 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-9 linux-libc-dev_3.2.16-1 login_1:4.1.5-1 lsb-base_4.1+Debian3 m4_1.4.16-3 make_3.81-8.2 man-db_2.6.1-2 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-4 multiarch-support_2.13-32 ncurses-base_5.9-7 ncurses-bin_5.9-7 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-10 perl-base_5.14.2-10 perl-modules_5.14.2-10 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc2-2.1 python2.7-minimal_2.7.3~rc2-2.1 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-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-1 zlib1g-dev_1:1.2.7.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -281,13 +350,10 @@ Package versions: apt_0.8.15.9 autoconf_2.68-1 automake_1:1.11.1-1 autotools-dev
Unpack source
─────────────
-gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-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_1.3.0-1.dsc
+dpkg-source: warning: extracting unsigned source package (cufflinks_1.3.0-2.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: unpacking cufflinks_1.3.0-2.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
@@ -307,7 +373,7 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-48ef29fa-8362-4a84-aa4d-3f35ec1f65b0
+SCHROOT_SESSION_ID=sid-amd64-sbuild-c0f656a9-be50-4fae-a8c6-6763088b32b6
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -319,7 +385,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package cufflinks
-dpkg-buildpackage: source version 1.3.0-1
+dpkg-buildpackage: source version 1.3.0-2
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
dpkg-source --before-build cufflinks-1.3.0
dpkg-buildpackage: host architecture amd64
@@ -336,59 +402,59 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
dpkg-source -b cufflinks-1.3.0
dpkg-source: info: using source format `3.0 (quilt)'
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
+dpkg-source: info: building cufflinks in cufflinks_1.3.0-2.debian.tar.gz
+dpkg-source: info: building cufflinks in cufflinks_1.3.0-2.dsc
debian/rules build
dh build --with autoreconf
dh_testdir
dh_autoreconf
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
-../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from...
-../../lib/autoconf/general.m4:2591: _AC_COMPILE_IFELSE is expanded from...
-../../lib/autoconf/general.m4:2607: AC_COMPILE_IFELSE is expanded from...
-../../lib/m4sugar/m4sh.m4:606: AS_IF is expanded from...
-../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from...
-../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from...
+../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
+../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
+../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
+../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
+../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
+../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
-../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from...
-../../lib/autoconf/general.m4:2591: _AC_COMPILE_IFELSE is expanded from...
-../../lib/autoconf/general.m4:2607: AC_COMPILE_IFELSE is expanded from...
-../../lib/m4sugar/m4sh.m4:606: AS_IF is expanded from...
-../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from...
-../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from...
+../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
+../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
+../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
+../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
+../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
+../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
-../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from...
-../../lib/autoconf/general.m4:2591: _AC_COMPILE_IFELSE is expanded from...
-../../lib/autoconf/general.m4:2607: AC_COMPILE_IFELSE is expanded from...
-../../lib/m4sugar/m4sh.m4:606: AS_IF is expanded from...
-../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from...
-../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from...
+../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
+../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
+../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
+../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
+../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
+../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
-../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from...
-../../lib/autoconf/general.m4:2591: _AC_COMPILE_IFELSE is expanded from...
-../../lib/autoconf/general.m4:2607: AC_COMPILE_IFELSE is expanded from...
-../../lib/m4sugar/m4sh.m4:606: AS_IF is expanded from...
-../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from...
-../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from...
+../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
+../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
+../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
+../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
+../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
+../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
-../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from...
-../../lib/autoconf/general.m4:2591: _AC_COMPILE_IFELSE is expanded from...
-../../lib/autoconf/general.m4:2607: AC_COMPILE_IFELSE is expanded from...
-../../lib/m4sugar/m4sh.m4:606: AS_IF is expanded from...
-../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from...
-../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from...
+../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
+../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
+../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
+../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
+../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
+../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:32: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
dh_auto_configure
@@ -475,7 +541,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode
-- 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 4.6.2-11) 4.6.2
+ GCC version: gcc (Debian 4.7.0-7) 4.7.0
Host System type: x86_64-pc-linux-gnu
Install prefix: /usr
Install eprefix: ${prefix}
@@ -495,7 +561,7 @@ In file included from abundances.h:22:0,
from clustering.cpp:10:
bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
+bundles.h:209:39: warning: 'boost::random::uniform_01<boost::random::mersenne_twister_engine<unsigned int, 32ul, 624ul, 397ul, 31ul, 2567483615u, 11ul, 4294967295u, 7ul, 2636928640u, 15ul, 4022730752u, 18ul, 1812433253u> > BundleFactory::_zeroone' [-Wreorder]
bundles.h:213:2: warning: when initialized here [-Wreorder]
In file included from clustering.h:38:0,
from clustering.cpp:10:
@@ -508,7 +574,7 @@ In file included from abundances.h:22:0,
from differential.cpp:17:
bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
+bundles.h:209:39: warning: 'boost::random::uniform_01<boost::random::mersenne_twister_engine<unsigned int, 32ul, 624ul, 397ul, 31ul, 2567483615u, 11ul, 4294967295u, 7ul, 2636928640u, 15ul, 4022730752u, 18ul, 1812433253u> > BundleFactory::_zeroone' [-Wreorder]
bundles.h:213:2: warning: when initialized here [-Wreorder]
In file included from differential.cpp:17:0:
abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
@@ -528,7 +594,7 @@ In file included from replicates.h:10:0,
from common.cpp:28:
bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
+bundles.h:209:39: warning: 'boost::random::uniform_01<boost::random::mersenne_twister_engine<unsigned int, 32ul, 624ul, 397ul, 31ul, 2567483615u, 11ul, 4294967295u, 7ul, 2636928640u, 15ul, 4022730752u, 18ul, 1812433253u> > BundleFactory::_zeroone' [-Wreorder]
bundles.h:213:2: warning: when initialized here [-Wreorder]
In file included from common.cpp:28:0:
replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
@@ -538,7 +604,7 @@ In file included from assemble.h:21:0,
from assemble.cpp:48:
bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
+bundles.h:209:39: warning: 'boost::random::uniform_01<boost::random::mersenne_twister_engine<unsigned int, 32ul, 624ul, 397ul, 31ul, 2567483615u, 11ul, 4294967295u, 7ul, 2636928640u, 15ul, 4022730752u, 18ul, 1812433253u> > BundleFactory::_zeroone' [-Wreorder]
bundles.h:213:2: warning: when initialized here [-Wreorder]
In file included from clustering.h:38:0,
from assemble.cpp:54:
@@ -547,729 +613,62 @@ 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]
assemble.cpp: In function 'void create_reachability_bp_graph(DAG&, ReachGraph&, std::vector<lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::BNode, std::allocator<lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::BNode> >, DagToBp&, const boost::adjacency_list<>&, const std::vector<bool>&)':
-assemble.cpp:188:21: warning: variable 'a_for_b' set but not used [-Wunused-but-set-variable]
assemble.cpp:123:17: warning: variable 'hits_for_node' set but not used [-Wunused-but-set-variable]
-assemble.cpp: In function 'void add_weights_to_reachability_bp_graph(ReachGraph&, const HitsForNodeMap&, const std::vector<Scaffold>&, const std::vector<Scaffold>&, lemon::BpUGraphExtender<lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase> >::UEdgeMap<long long int>&)':
-assemble.cpp:262:21: warning: variable 'a_for_b' 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 tokenize.o tokenize.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 abundances.o abundances.cpp
-In file included from abundances.h:22:0,
- from abundances.cpp:11:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from abundances.cpp:11:0:
-abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
-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]
-In file included from abundances.cpp:35:0:
-replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
-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:74:1: warning: when initialized here [-Wreorder]
-abundances.cpp: In member function 'virtual AbundanceStatus AbundanceGroup::status() const':
-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: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: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: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:2019:12: warning: unused variable 'num_salient_frags' [-Wunused-variable]
-abundances.cpp: In member function 'void AbundanceGroup::calculate_kappas()':
-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: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: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: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: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,
- from genes.cpp:10:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from genes.h:18:0,
- from genes.cpp:10:
-abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
-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 bundles.o bundles.cpp
-bundles.cpp:674:23: warning: integer constant is so large that it is unsigned [enabled by default]
-bundles.cpp:674:3: warning: this decimal constant is unsigned only in ISO C90 [enabled by default]
-In file included from bundles.cpp:16:0:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-bundles.cpp: In member function 'bool HitBundle::add_open_hit(boost::shared_ptr<const ReadGroupProperties>, const ReadHit*, bool)':
-bundles.cpp:294:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-bundles.cpp: In member function 'double BundleFactory::next_valid_alignment(const ReadHit*&)':
-bundles.cpp:714:18: warning: variable 'found_scaff' set but not used [-Wunused-but-set-variable]
-bundles.cpp:737:21: warning: unused variable 'a' [-Wunused-variable]
-bundles.cpp: In member function 'bool BundleFactory::next_bundle_hit_driven(HitBundle&)':
-bundles.cpp:793:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-bundles.cpp:793:37: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
-bundles.cpp: In member function 'bool BundleFactory::next_bundle_ref_driven(HitBundle&)':
-bundles.cpp:827:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-bundles.cpp:855:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-bundles.cpp:855:37: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
-bundles.cpp:853:16: warning: unused variable 't' [-Wunused-variable]
-bundles.cpp:842:8: warning: variable 'last_hit_ref_id_seen' set but not used [-Wunused-but-set-variable]
-bundles.cpp:843:6: warning: variable 'last_hit_pos_seen' 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 filters.o filters.cpp
-In file included from abundances.h:22:0,
- from genes.h:18,
- from filters.h:18,
- from filters.cpp:10:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from genes.h:18:0,
- from filters.h:18,
- from filters.cpp:10:
-abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
-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: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
-In file included from graph_optimize.h:17:0,
- from graph_optimize.cpp:13:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from genes.h:18:0,
- from filters.h:18,
- from graph_optimize.cpp:22:
-abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
-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]
-graph_optimize.cpp: In function 'bool collapse_contained_transfrags(std::vector<Scaffold>&, uint32_t)':
-graph_optimize.cpp:264:30: warning: variable 'e' 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 biascorrection.o biascorrection.cpp
-In file included from abundances.h:22:0,
- from biascorrection.cpp:12:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from biascorrection.cpp:12:0:
-abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
-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]
-locfit/adap.c: In function 'aband3':
-locfit/adap.c:157:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
-locfit/adap.c:157:14: warning: variable 'd' set but not used [-Wunused-but-set-variable]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o ar_funs.o `test -f 'locfit/ar_funs.c' || echo './'`locfit/ar_funs.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o arith.o `test -f 'locfit/arith.c' || echo './'`locfit/arith.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o band.o `test -f 'locfit/band.c' || echo './'`locfit/band.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o c_args.o `test -f 'locfit/c_args.c' || echo './'`locfit/c_args.c
-locfit/c_args.c: In function 'readilist':
-locfit/c_args.c:58:13: warning: variable 'nd' set but not used [-Wunused-but-set-variable]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o c_plot.o `test -f 'locfit/c_plot.c' || echo './'`locfit/c_plot.c
-locfit/c_plot.c: In function 'plotfit':
-locfit/c_plot.c:228:13: warning: variable 'sd' set but not used [-Wunused-but-set-variable]
-locfit/c_plot.c:226:36: warning: variable 'sef' set but not used [-Wunused-but-set-variable]
-locfit/c_plot.c: In function 'setplot':
-locfit/c_plot.c:470:3: warning: passing argument 1 of 'setvarname' from incompatible pointer type [enabled by default]
-locfit/vari.hpp:23:10: note: expected 'struct vari *' but argument is of type 'char *'
-locfit/c_plot.c: In function 'plotfit':
-locfit/c_plot.c:364:45: warning: 'iy' may be used uninitialized in this function [-Wuninitialized]
-locfit/c_plot.c:361:43: warning: 'ix' may be used uninitialized in this function [-Wuninitialized]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o cmd.o `test -f 'locfit/cmd.c' || echo './'`locfit/cmd.c
-locfit/cmd.c: In function 'ckap':
-locfit/cmd.c:101:10: warning: variable 'nd' set but not used [-Wunused-but-set-variable]
-locfit/cmd.c: In function 'predict':
-locfit/cmd.c:197:13: warning: variable 'data' set but not used [-Wunused-but-set-variable]
-locfit/cmd.c: In function 'setcolor':
-locfit/cmd.c:447:5: warning: 'return' with a value, in function returning void [enabled by default]
-locfit/cmd.c: In function 'cmdint':
-locfit/cmd.c:675:19: warning: variable 'nr' set but not used [-Wunused-but-set-variable]
-locfit/cmd.c: In function 'table':
-locfit/cmd.c:528:17: warning: 'ix' may be used uninitialized in this function [-Wuninitialized]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o dens_haz.o `test -f 'locfit/dens_haz.c' || echo './'`locfit/dens_haz.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o dens_int.o `test -f 'locfit/dens_int.c' || echo './'`locfit/dens_int.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o dens_odi.o `test -f 'locfit/dens_odi.c' || echo './'`locfit/dens_odi.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o density.o `test -f 'locfit/density.c' || echo './'`locfit/density.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o dist.o `test -f 'locfit/dist.c' || echo './'`locfit/dist.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o ev_atree.o `test -f 'locfit/ev_atree.c' || echo './'`locfit/ev_atree.c
-locfit/ev_atree.c: In function 'atree_int':
-locfit/ev_atree.c:203:3: warning: 'nc' may be used uninitialized in this function [-Wuninitialized]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o ev_interp.o `test -f 'locfit/ev_interp.c' || echo './'`locfit/ev_interp.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o ev_kdtre.o `test -f 'locfit/ev_kdtre.c' || echo './'`locfit/ev_kdtre.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o ev_main.o `test -f 'locfit/ev_main.c' || echo './'`locfit/ev_main.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o ev_trian.o `test -f 'locfit/ev_trian.c' || echo './'`locfit/ev_trian.c
-locfit/ev_trian.c: In function 'triang_grow.constprop.0':
-locfit/ev_trian.c:59:55: warning: 'im' may be used uninitialized in this function [-Wuninitialized]
-locfit/ev_trian.c:59:59: warning: 'jm' may be used uninitialized in this function [-Wuninitialized]
-locfit/ev_trian.c: In function 'triang_grow':
-locfit/ev_trian.c:59:59: warning: 'jm' may be used uninitialized in this function [-Wuninitialized]
-locfit/ev_trian.c:59:55: warning: 'im' may be used uninitialized in this function [-Wuninitialized]
-locfit/ev_trian.c: In function 'triang_descend':
-locfit/ev_trian.c:110:49: warning: 'jm' may be used uninitialized in this function [-Wuninitialized]
-locfit/ev_trian.c:110:45: warning: 'im' may be used uninitialized in this function [-Wuninitialized]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o family.o `test -f 'locfit/family.c' || echo './'`locfit/family.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o fitted.o `test -f 'locfit/fitted.c' || echo './'`locfit/fitted.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o frend.o `test -f 'locfit/frend.c' || echo './'`locfit/frend.c
-locfit/frend.c: In function 'procvvord':
-locfit/frend.c:205:39: warning: variable 'ip' set but not used [-Wunused-but-set-variable]
-locfit/frend.c:204:48: warning: variable 't2' set but not used [-Wunused-but-set-variable]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o help.o `test -f 'locfit/help.c' || echo './'`locfit/help.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o lf_dercor.o `test -f 'locfit/lf_dercor.c' || echo './'`locfit/lf_dercor.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o lf_fitfun.o `test -f 'locfit/lf_fitfun.c' || echo './'`locfit/lf_fitfun.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o lf_robust.o `test -f 'locfit/lf_robust.c' || echo './'`locfit/lf_robust.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o lf_vari.o `test -f 'locfit/lf_vari.c' || echo './'`locfit/lf_vari.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o lfd.o `test -f 'locfit/lfd.c' || echo './'`locfit/lfd.c
-locfit/lfd.c: In function 'setfilename':
-locfit/lfd.c:60:7: warning: zero-length gnu_printf format string [-Wformat-zero-length]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o lfstr.o `test -f 'locfit/lfstr.c' || echo './'`locfit/lfstr.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o linalg.o `test -f 'locfit/linalg.c' || echo './'`locfit/linalg.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o locfit.o `test -f 'locfit/locfit.c' || echo './'`locfit/locfit.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o m_chol.o `test -f 'locfit/m_chol.c' || echo './'`locfit/m_chol.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o m_eigen.o `test -f 'locfit/m_eigen.c' || echo './'`locfit/m_eigen.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o m_jacob.o `test -f 'locfit/m_jacob.c' || echo './'`locfit/m_jacob.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o m_max.o `test -f 'locfit/m_max.c' || echo './'`locfit/m_max.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o makecmd.o `test -f 'locfit/makecmd.c' || echo './'`locfit/makecmd.c
-locfit/makecmd.c: In function 'makefields':
-locfit/makecmd.c:88:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o math.o `test -f 'locfit/math.c' || echo './'`locfit/math.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o minmax.o `test -f 'locfit/minmax.c' || echo './'`locfit/minmax.c
-locfit/minmax.c: In function 'updatesd':
-locfit/minmax.c:94:21: warning: 'sd' may be used uninitialized in this function [-Wuninitialized]
-locfit/minmax.c: In function 'findab':
-locfit/minmax.c:217:8: warning: 'sing' may be used uninitialized in this function [-Wuninitialized]
-locfit/minmax.c:164:19: note: 'sing' was declared here
-locfit/minmax.c: In function 'mmax':
-locfit/minmax.c:217:8: warning: 'sing' may be used uninitialized in this function [-Wuninitialized]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o nbhd.o `test -f 'locfit/nbhd.c' || echo './'`locfit/nbhd.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o pcomp.o `test -f 'locfit/pcomp.c' || echo './'`locfit/pcomp.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o pout.o `test -f 'locfit/pout.c' || echo './'`locfit/pout.c
-locfit/pout.c: In function 'plotxwin':
-locfit/pout.c:447:38: warning: variable 'vz' set but not used [-Wunused-but-set-variable]
-locfit/pout.c:447:34: warning: variable 'vy' set but not used [-Wunused-but-set-variable]
-locfit/pout.c:447:30: warning: variable 'vx' set but not used [-Wunused-but-set-variable]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o preplot.o `test -f 'locfit/preplot.c' || echo './'`locfit/preplot.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o random.o `test -f 'locfit/random.c' || echo './'`locfit/random.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o readfile.o `test -f 'locfit/readfile.c' || echo './'`locfit/readfile.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o scb.o `test -f 'locfit/scb.c' || echo './'`locfit/scb.c
-locfit/scb.c: In function 'cumulant':
-locfit/scb.c:61:10: warning: variable 'b2i' set but not used [-Wunused-but-set-variable]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o scb_cons.o `test -f 'locfit/scb_cons.c' || echo './'`locfit/scb_cons.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o simul.o `test -f 'locfit/simul.c' || echo './'`locfit/simul.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o solve.o `test -f 'locfit/solve.c' || echo './'`locfit/solve.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o startlf.o `test -f 'locfit/startlf.c' || echo './'`locfit/startlf.c
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o strings.o `test -f 'locfit/strings.c' || echo './'`locfit/strings.c
-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 vari.o `test -f 'locfit/vari.cpp' || echo './'`locfit/vari.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 wdiag.o `test -f 'locfit/wdiag.c' || echo './'`locfit/wdiag.c
-locfit/wdiag.c: In function 'wdiag':
-locfit/wdiag.c:109:18: warning: 'lxd' may be used uninitialized in this function [-Wuninitialized]
-gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -c -o weight.o `test -f 'locfit/weight.c' || echo './'`locfit/weight.c
-locfit/weight.c: In function 'weightdd':
-locfit/weight.c:162:10: warning: variable 'w' 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 replicates.o replicates.cpp
-In file included from replicates.h:10:0,
- from replicates.cpp:15:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from replicates.cpp:15:0:
-replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
-replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable]
-replicates.cpp: In member function 'virtual double MassDispersionModel::scale_mass_variance(double) const':
-replicates.cpp:139:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-replicates.cpp:143:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-replicates.cpp: In function 'boost::shared_ptr<const MassDispersionModel> fit_dispersion_model_helper(const string&, const std::vector<double>&, const std::vector<LocusCountList>&)':
-replicates.cpp:253:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-replicates.cpp:263:34: warning: variable 'p' set but not used [-Wunused-but-set-variable]
-replicates.cpp:318:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-replicates.cpp:333:30: warning: variable 'p' set but not used [-Wunused-but-set-variable]
-replicates.cpp: In function 'boost::shared_ptr<const MassDispersionModel> fit_dispersion_model(const string&, const std::vector<double>&, const std::vector<LocusCountList>&)':
-replicates.cpp:379:28: 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 multireads.o multireads.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 jensen_shannon.o jensen_shannon.cpp
-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 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
-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 GBase.o GBase.cpp
-GBase.cpp: In function 'int saprintf(char**, const char*, ...)':
-GBase.cpp:46:35: warning: 'buf' may be used uninitialized in this function [-Wuninitialized]
-GBase.cpp: In function 'char* Gsubstr(const char*, char*, char*)':
-GBase.cpp:271:29: warning: 'subs' may be used uninitialized in this function [-Wuninitialized]
-GBase.cpp: In function 'char* upCase(const char*)':
-GBase.cpp:397:11: warning: 'upstr' may be used uninitialized in this function [-Wuninitialized]
-GBase.cpp: In function 'char* loCase(const char*)':
-GBase.cpp:407:11: warning: 'lostr' may be used uninitialized in this function [-Wuninitialized]
-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 gdna.o gdna.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 GStr.o GStr.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 GFaSeqGet.o GFaSeqGet.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 GFastaIndex.o GFastaIndex.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 gff.o gff.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 gff_utils.o gff_utils.cpp
-gff_utils.cpp: In function 'void placeGf(GffObj*, GenomicSeqData*, bool, bool, bool, bool)':
-gff_utils.cpp:348:7: warning: variable 'tidx' 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 gtf_tracking.o gtf_tracking.cpp
-rm -f libgc.a
-ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o
-ranlib libgc.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 cufflinks.o cufflinks.cpp
-In file included from abundances.h:22:0,
- from clustering.h:38,
- from cufflinks.cpp:26:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from clustering.h:38:0,
- from cufflinks.cpp:26:
-abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
-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]
-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: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: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:1201:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
-cufflinks.cpp: In function 'bool assemble_hits(BundleFactory&, BiasLearner*)':
-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: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: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:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from cuffdiff.cpp:28:0:
-abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
-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]
-In file included from differential.h:29:0,
- from cuffdiff.cpp:42:
-replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
-replicates.h:141:50: warning: unused variable 's2' [-Wunused-variable]
-cuffdiff.cpp: In function 'void print_FPKM_tracking(FILE*, const FPKMTrackingTable&)':
-cuffdiff.cpp:492:25: warning: variable 'status' set but not used [-Wunused-but-set-variable]
-cuffdiff.cpp: In function 'void driver(FILE*, FILE*, std::vector<std::basic_string<char> >&, Outfiles&)':
-cuffdiff.cpp:901:10: warning: variable 'single_replicate_fac' set but not used [-Wunused-but-set-variable]
-g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -L/usr/lib -o cuffdiff cuffdiff.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 gtf_to_sam.o gtf_to_sam.cpp
-In file included from gtf_to_sam.cpp:29:0:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-gtf_to_sam.cpp: In function 'void print_scaff_as_sam(FILE*, const RefSequenceTable&, const Scaffold&)':
-gtf_to_sam.cpp:148:100: warning: format '%d' expects argument of type 'int', but argument 3 has type 'RefID {aka long unsigned int}' [-Wformat]
-g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -L/usr/lib -o gtf_to_sam gtf_to_sam.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 compress_gtf.o compress_gtf.cpp
-In file included from compress_gtf.cpp:30:0:
-bundles.h: In constructor 'BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)':
-bundles.h:363:9: warning: 'BundleFactory::_curr_bundle' will be initialized after [-Wreorder]
-bundles.h:209:39: warning: 'boost::uniform_01<boost::random::mersenne_twister<unsigned int, 32, 624, 397, 31, 2567483615u, 11, 7, 2636928640u, 15, 4022730752u, 18, 3346425566u> > BundleFactory::_zeroone' [-Wreorder]
-bundles.h:213:2: warning: when initialized here [-Wreorder]
-In file included from genes.h:18:0,
- from compress_gtf.cpp:35:
-abundances.h: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)':
-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++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -L/usr/lib -o compress_gtf compress_gtf.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 gffread.o gffread.cpp
-g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include -o gffread gffread.o libgc.a -lz
+In file included from ./lemon/list_graph.h:26:0,
+ from ./lemon/dfs.h:26,
+ from ./lemon/topology.h:22,
+ from assemble.cpp:19:
+./lemon/bits/base_extender.h: In instantiation of 'lemon::BidirBpUGraphExtender<Base>::Node lemon::BidirBpUGraphExtender<Base>::source(const UEdge&) const [with Base = lemon::SmartBpUGraphBase; lemon::BidirBpUGraphExtender<Base>::Node = lemon::SmartBpUGraphBase::Node; lemon::BidirBpUGraphExtender<Base>::UEdge = lemon::SmartBpUGraphBase::UEdge]':
+assemble.cpp:258:36: required from here
+./lemon/bits/base_extender.h:362:21: error: 'aNode' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
+./lemon/bits/base_extender.h:362:21: note: declarations in dependent base 'lemon::SmartBpUGraphBase' are not found by unqualified lookup
+./lemon/bits/base_extender.h:362:21: note: use 'this->aNode' instead
+./lemon/bits/base_extender.h: In instantiation of 'lemon::BidirBpUGraphExtender<Base>::Node lemon::BidirBpUGraphExtender<Base>::target(const UEdge&) const [with Base = lemon::SmartBpUGraphBase; lemon::BidirBpUGraphExtender<Base>::Node = lemon::SmartBpUGraphBase::Node; lemon::BidirBpUGraphExtender<Base>::UEdge = lemon::SmartBpUGraphBase::UEdge]':
+assemble.cpp:259:36: required from here
+./lemon/bits/base_extender.h:365:21: error: 'bNode' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
+./lemon/bits/base_extender.h:365:21: note: declarations in dependent base 'lemon::SmartBpUGraphBase' are not found by unqualified lookup
+./lemon/bits/base_extender.h:365:21: note: use 'this->bNode' instead
+make[3]: *** [assemble.o] Error 1
make[3]: Leaving directory `/«PKGBUILDDIR»/src'
-make[3]: Entering directory `/«PKGBUILDDIR»'
-make[3]: Nothing to be done for `all-am'.
-make[3]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
- dh_auto_test
-make[1]: Entering directory `/«PKGBUILDDIR»'
-Making check in src
-make[2]: Entering directory `/«PKGBUILDDIR»/src'
-make[2]: Nothing to be done for `check'.
-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»'
- fakeroot debian/rules binary
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-dh binary --with autoreconf
- dh_testroot
- dh_prep
- dh_installdirs
- dh_auto_install
-make[1]: Entering directory `/«PKGBUILDDIR»'
-Making install in src
-make[2]: Entering directory `/«PKGBUILDDIR»/src'
-make[3]: Entering directory `/«PKGBUILDDIR»/src'
-test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/cufflinks/usr/bin"
- /usr/bin/install -c cufflinks cuffcompare cuffdiff gtf_to_sam compress_gtf gffread '/«PKGBUILDDIR»/debian/cufflinks/usr/bin'
-test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/cufflinks/usr/bin"
- /usr/bin/install -c cuffmerge '/«PKGBUILDDIR»/debian/cufflinks/usr/bin'
-make[3]: Nothing to be done for `install-data-am'.
-make[3]: Leaving directory `/«PKGBUILDDIR»/src'
-make[2]: Leaving directory `/«PKGBUILDDIR»/src'
-make[2]: Entering directory `/«PKGBUILDDIR»'
-make[3]: Entering directory `/«PKGBUILDDIR»'
-make[3]: Nothing to be done for `install-exec-am'.
-make[3]: Nothing to be done for `install-data-am'.
-make[3]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: *** [all] Error 2
make[1]: Leaving directory `/«PKGBUILDDIR»'
- dh_install
- dh_installdocs
- dh_installchangelogs
- dh_installexamples
- dh_installman
- dh_installcatalogs
- dh_installcron
- dh_installdebconf
- dh_installemacsen
- dh_installifupdown
- dh_installinfo
- dh_installinit
- dh_installmenu
- dh_installmime
- dh_installmodules
- dh_installlogcheck
- dh_installlogrotate
- dh_installpam
- dh_installppp
- dh_installudev
- dh_installwm
- dh_installxfonts
- dh_installgsettings
- dh_bugfiles
- dh_ucf
- dh_lintian
- dh_gconf
- dh_icons
- dh_perl
- dh_usrlocal
- dh_link
- dh_compress
- dh_fixperms
- dh_strip
- dh_makeshlibs
- dh_shlibdeps
- dh_installdeb
- dh_gencontrol
- dh_md5sums
- debian/rules override_dh_builddeb
-make[1]: Entering directory `/«PKGBUILDDIR»'
-dh_builddeb -- -Z xz
-dpkg-deb: building package `cufflinks' in `../cufflinks_1.3.0-1_amd64.deb'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
- dpkg-genchanges >../cufflinks_1.3.0-1_amd64.changes
-dpkg-genchanges: including full source code in upload
- dpkg-source --after-build cufflinks-1.3.0
-dpkg-buildpackage: full upload (original source is included)
+dh_auto_build: make -j1 returned exit code 2
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120106-0929
+Build finished at 20120509-0840
Finished
────────
-I: Built successfully
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-cufflinks_1.3.0-1_amd64.changes:
-────────────────────────────────
-
-Format: 1.8
-Date: Fri, 06 Jan 2012 09:20:23 +0900
-Source: cufflinks
-Binary: cufflinks
-Architecture: source amd64
-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
-Changes:
- cufflinks (1.3.0-1) unstable; urgency=low
- .
- [ Alexandre Mestiashvili ]
- * New upstream release
- * Fixed spelling error.
- * Updated source version
- .
- [ Charles Plessy ]
- * Removed quilt patch management, and rely on dpkg-dev exclusively.
-Checksums-Sha1:
- 2779854ef842ec7935699e617543e9a178a13e5f 1295 cufflinks_1.3.0-1.dsc
- fa93a7a33f0649793ec1d185cb7043fd0dc2018b 676660 cufflinks_1.3.0.orig.tar.gz
- d91e15de00c0ff20b7b8a94e5a76be5d97eef648 11608 cufflinks_1.3.0-1.debian.tar.gz
- fc99b39dcc94ff567def73c48fd2973aac381dd1 1003092 cufflinks_1.3.0-1_amd64.deb
-Checksums-Sha256:
- a36abde47b6fc75061852d47ce19359ad41e83aef46851a5b1f1717196629ad5 1295 cufflinks_1.3.0-1.dsc
- c1e194e30e6ba2e1cbbd35e5f92be59f9fdef95a12079b3141790efbbdbdfd86 676660 cufflinks_1.3.0.orig.tar.gz
- d34e3b343599fb1726c15d31f38e61a18e5b4ae80d4d3c17f63b8754e153efb1 11608 cufflinks_1.3.0-1.debian.tar.gz
- 711a233ac3ca720cb061c08ce781724172c37b0f7b2d20437818cd2888bf8522 1003092 cufflinks_1.3.0-1_amd64.deb
-Files:
- 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_1.3.0-1_amd64.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 1003092 bytes: control archive= 1199 bytes.
- 870 bytes, 16 lines control
- 1123 bytes, 18 lines md5sums
- Package: cufflinks
- Version: 1.3.0-1
- Architecture: amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- 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
- Priority: optional
- Homepage: http://cufflinks.cbcb.umd.edu/
- Description: Transcript assembly, differential expression and regulation for RNA-Seq
- Cufflinks assembles transcripts, estimates their abundances, and tests for
- differential expression and regulation in RNA-Seq samples. It accepts aligned
- RNA-Seq reads and assembles the alignments into a parsimonious set of
- transcripts. Cufflinks then estimates the relative abundances of these
- transcripts based on how many reads support each one.
-
-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 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
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-lintian
-───────
-
-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 ang and
-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
-
-I: Lintian run was successful.
+E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
-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:
- 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*
- 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 ...
-Removing autoconf ...
-Purging configuration files for autoconf ...
-Removing libtool ...
-Removing autotools-dev ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libbam-dev ...
-Removing libboost-thread-dev ...
-Removing libboost-thread1.46-dev ...
-Removing libboost-date-time1.46-dev ...
-Removing libboost-date-time1.46.1 ...
-Purging configuration files for libboost-date-time1.46.1 ...
-Removing libboost-dev ...
-Removing libboost-serialization1.46-dev ...
-Removing libboost-serialization1.46.1 ...
-Purging configuration files for libboost-serialization1.46.1 ...
-Removing libboost-thread1.46.1 ...
-Purging configuration files for libboost-thread1.46.1 ...
-Removing libboost1.46-dev ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing python ...
-Purging configuration files for python ...
-Removing python2.7 ...
-Purging configuration files for python2.7 ...
-Removing libexpat1 ...
-Purging configuration files for libexpat1 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libffi5 ...
-Purging configuration files for libffi5 ...
-Removing libicu48 ...
-Purging configuration files for libicu48 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libncursesw5 ...
-Purging configuration files for libncursesw5 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libsqlite3-0 ...
-Purging configuration files for libsqlite3-0 ...
-Removing python-minimal ...
-Removing python2.7-minimal ...
-Purging configuration files for python2.7-minimal ...
-Removing libssl1.0.0 ...
-Purging configuration files for libssl1.0.0 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing m4 ...
-Removing mime-support ...
-Purging configuration files for mime-support ...
-Removing sbuild-build-depends-core-dummy ...
-Removing zlib1g-dev ...
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 207816
-Build-Time: 487
+Build-Space: 14932
+Build-Time: 62
Distribution: unstable
-Install-Time: 20
-Job: cufflinks_1.3.0-1.dsc
-Lintian: pass
+Fail-Stage: build
+Install-Time: 168
+Job: cufflinks_1.3.0-2.dsc
Package: cufflinks
-Package-Time: 513
-Source-Version: 1.3.0-1
-Space: 207816
-Status: successful
-Version: 1.3.0-1
+Package-Time: 257
+Source-Version: 1.3.0-2
+Space: 14932
+Status: attempted
+Version: 1.3.0-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120106-0929
-Build needed 00:08:33, 207816k disc space
+Finished at 20120509-0840
+Build needed 00:04:17, 14932k disc space
--
Transcript assembly, differential expression, and differential regulation for RNA-Seq.
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