[med-svn] [SCM] cufflinks branch, builds/amd64, updated. builds/amd64/1.3.0-1-2-g2eb7524

Thu May 24 03:58:29 UTC 2012

The following commit has been merged in the builds/amd64 branch:
commit 2eb7524de190d349c038dc6c97b2091fecae03e7
Author: Charles Plessy <plessy at debian.org>
Date:   Thu May 24 12:55:28 2012 +0900

    cufflinks (1.3.0-2) unstable; urgency=low

diff --git a/changes b/changes
index f9e15a4..77647ed 100644
--- a/changes
+++ b/changes
@@ -2,57 +2,59 @@
 Hash: SHA256
 
 Format: 1.8
-Date: Fri, 06 Jan 2012 09:20:23 +0900
+Date: Thu, 24 May 2012 12:36:16 +0900
 Source: cufflinks
 Binary: cufflinks
 Architecture: source amd64
-Version: 1.3.0-1
+Version: 1.3.0-2
 Distribution: unstable
 Urgency: low
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Changed-By: Charles Plessy <plessy at debian.org>
 Description: 
  cufflinks  - Transcript assembly, differential expression and regulation for R
+Closes: 672744
 Changes: 
- cufflinks (1.3.0-1) unstable; urgency=low
- .
-   [ Alexandre Mestiashvili ]
-   * New upstream release
-   * Fixed spelling error.
-   * Updated source version
+ cufflinks (1.3.0-2) unstable; urgency=low
  .
    [ Charles Plessy ]
-   * Removed quilt patch management, and rely on dpkg-dev exclusively.
+   * Normalised and summarised debian/copyright.
+ .
+   [ Carlos Borroto ]
+   * Added tophat to Enhances
+ .
+   [ Andreas Tille ]
+   * debian/upstream: Added references as specified in tasks file
+   * debian/copyright: Added Upstream-Contact e-mail
+   * debian/patches/gcc-4.7.patch: Fix gcc-4.7 build issue
+     Closes: #672744
 Checksums-Sha1: 
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- 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
+ 430ccc844be1e456c4a8438133a7816d0b7f3c14 2181 cufflinks_1.3.0-2.dsc
+ 08c909b4f179977b620dc9037e0e9fd610ef653a 12997 cufflinks_1.3.0-2.debian.tar.gz
+ a787cff4ebebecd73e50c4112853b6ec76d30350 1042604 cufflinks_1.3.0-2_amd64.deb
 Checksums-Sha256: 
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- c1e194e30e6ba2e1cbbd35e5f92be59f9fdef95a12079b3141790efbbdbdfd86 676660 cufflinks_1.3.0.orig.tar.gz
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- 711a233ac3ca720cb061c08ce781724172c37b0f7b2d20437818cd2888bf8522 1003092 cufflinks_1.3.0-1_amd64.deb
+ 5c9ecd96935ea742de0c7c4c0bde457ead5a2abf303a8ac15c425685e73da0b7 2181 cufflinks_1.3.0-2.dsc
+ 1bb5d58a1eaeacecf56a36955ee35436a941a8e4234af079ac5e9be91802b4e4 12997 cufflinks_1.3.0-2.debian.tar.gz
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 Files: 
- e42daabe1e33d7e911cb8a64968e0d06 2181 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
+ afa7ee886a2309eae14051afeae2a5b8 2181 non-free/science optional cufflinks_1.3.0-2.dsc
+ 272aa1a9e3ae79935641e3cb45c2ec3c 12997 non-free/science optional cufflinks_1.3.0-2.debian.tar.gz
+ b4ea215faae024f44c6d5b2d9186c4a7 1042604 non-free/science optional cufflinks_1.3.0-2_amd64.deb
 
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diff --git a/dsc b/dsc
index d9faeec..b82e88c 100644
--- a/dsc
+++ b/dsc
@@ -1,45 +1,24 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
-
 Format: 3.0 (quilt)
 Source: cufflinks
 Binary: cufflinks
 Architecture: any
-Version: 1.3.0-1
+Version: 1.2.1-1
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>, Andreas Tille <tille at debian.org>, Charles Plessy <plessy at debian.org>
+Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>, Andreas Tille <tille at debian.org>
 Dm-Upload-Allowed: yes
 Homepage: http://cufflinks.cbcb.umd.edu/
 Standards-Version: 3.9.2
 Vcs-Browser: http://git.debian.org/?p=debian-med/cufflinks.git;a=summary
 Vcs-Git: git://git.debian.org/debian-med/cufflinks.git
-Build-Depends: debhelper (>= 8), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python (>= 2.6.6-3~)
+Build-Depends: debhelper (>= 8), autotools-dev, libboost-dev (>= 1.38.0), libboost-thread-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, quilt (>= 0.46-7~), python (>= 2.6.6-3~)
 Package-List: 
- cufflinks deb non-free/science optional
+ cufflinks deb science optional
 Checksums-Sha1: 
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- d91e15de00c0ff20b7b8a94e5a76be5d97eef648 11608 cufflinks_1.3.0-1.debian.tar.gz
+ 6439059aafd2bbbce582f027e2283f5886559d9d 673097 cufflinks_1.2.1.orig.tar.gz
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 Checksums-Sha256: 
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 Files: 
- 6914059cf8c8f22eb388e1fde44deabe 676660 cufflinks_1.3.0.orig.tar.gz
- 44296465461c9626c80056250d8bb018 11608 cufflinks_1.3.0-1.debian.tar.gz
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diff --git a/log b/log
index 82d67dd..caadb4a 100644
--- a/log
+++ b/log
@@ -1,7 +1,7 @@
-sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on aqwa.igloo
+sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on anx191
 
 ╔══════════════════════════════════════════════════════════════════════════════╗
-║ cufflinks 1.3.0-2 (amd64)                                  09 mai 2012 08:36 ║
+║ cufflinks 1.3.0-2 (amd64)                                  24 May 2012 12:43 ║
 ╚══════════════════════════════════════════════════════════════════════════════╝
 
 Package: cufflinks
@@ -10,41 +10,23 @@ Source Version: 1.3.0-2
 Distribution: unstable
 Architecture: amd64
 
-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»'
+I: NOTICE: Log filtering will replace 'build/cufflinks-n_AxGv/cufflinks-1.3.0' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/cufflinks-n_AxGv' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-4f66719b-7332-4727-9026-c91ab1d92a86' with '«CHROOT»'
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
 │ Update chroot                                                                │
 └──────────────────────────────────────────────────────────────────────────────┘
 
-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)
+Hit ftp://ftp.jaist.ac.jp sid InRelease
+Get:1 ftp://ftp.jaist.ac.jp sid/main amd64 Packages/DiffIndex [7876 B]
+Get:2 ftp://ftp.jaist.ac.jp sid/main Translation-en/DiffIndex [7876 B]
+Fetched 15.8 kB in 3s (5239 B/s)
 Reading package lists...
 Reading package lists...
 Building dependency tree...
 Reading state information...
-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) ...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
 │ Fetch source files                                                           │
@@ -61,7 +43,7 @@ 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-BMLHA3/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-tDhVMr/apt_archive/sbuild-build-depends-core-dummy.deb'.
 OK
 Reading package lists...
 
@@ -73,22 +55,14 @@ Installing build dependencies
 Reading package lists...
 Building dependency tree...
 Reading state information...
+sbuild-build-depends-core-dummy is already the newest version.
 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
-0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
-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 ... 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) ...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 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-Y1AF0V/apt_archive/sbuild-build-depends-cufflinks-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-cufflinks-dummy' in `/«BUILDDIR»/resolver-LdYcsz/apt_archive/sbuild-build-depends-cufflinks-dummy.deb'.
 OK
 Reading package lists...
 
@@ -101,9 +75,9 @@ Reading package lists...
 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 libasprintf0c2
-  libbam-dev libboost-date-time1.49-dev libboost-date-time1.49.0 libboost-dev
+  autoconf automake autotools-dev debhelper dh-autoreconf file 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
@@ -111,12 +85,11 @@ The following extra packages will be installed:
   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 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
+  autoconf2.13 autoconf-archive gnu-standards autoconf-doc 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
@@ -124,12 +97,12 @@ Suggested packages:
   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
+  autopoint curl wget lynx-cur libglib2.0-data shared-mime-info 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 libasprintf0c2
-  libbam-dev libboost-date-time1.49-dev libboost-date-time1.49.0 libboost-dev
+  autoconf automake autotools-dev debhelper dh-autoreconf file 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
@@ -137,72 +110,71 @@ The following NEW packages will be installed:
   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]
+0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded.
+Need to get 35.5 MB/37.1 MB of archives.
+After this operation, 171 MB of additional disk space will be used.
+Get:1 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libncursesw5 amd64 5.9-7 [140 kB]
+Get:2 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libpipeline1 amd64 1.2.1-1 [39.2 kB]
+Get:3 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libssl1.0.0 amd64 1.0.1c-1 [1211 kB]
+Get:4 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libasprintf0c2 amd64 0.18.1.1-8 [26.6 kB]
+Get:5 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libmagic1 amd64 5.11-1 [250 kB]
+Get:6 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libpcre3 amd64 1:8.30-5 [242 kB]
+Get:7 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libsqlite3-0 amd64 3.7.12.1-1 [453 kB]
+Get:8 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libxml2 amd64 2.7.8.dfsg-9.1 [897 kB]
+Get:9 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libglib2.0-0 amd64 2.32.3-1 [2081 kB]
+Get:10 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libcroco3 amd64 0.6.5-1 [151 kB]
+Get:11 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libexpat1 amd64 2.1.0-1 [141 kB]
+Get:12 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libgettextpo0 amd64 0.18.1.1-8 [144 kB]
+Get:13 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libicu48 amd64 4.8.1.1-6 [8131 kB]
+Get:14 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main groff-base amd64 1.21-7 [1151 kB]
+Get:15 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main man-db amd64 2.6.1-2 [1057 kB]
+Get:16 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main file amd64 5.11-1 [53.2 kB]
+Get:17 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main gettext-base amd64 0.18.1.1-8 [153 kB]
+Get:18 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main m4 amd64 1.4.16-3 [260 kB]
+Get:19 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main mime-support all 3.52-1 [35.5 kB]
+Get:20 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main python2.7-minimal amd64 2.7.3~rc2-2.1 [1770 kB]
+Get:21 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main python2.7 amd64 2.7.3~rc2-2.1 [2716 kB]
+Get:22 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:23 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main python all 2.7.2-10 [177 kB]
+Get:24 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main autoconf all 2.69-1 [589 kB]
+Get:25 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main autotools-dev all 20120210.1 [72.7 kB]
+Get:26 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main automake all 1:1.11.5-1 [606 kB]
+Get:27 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main gettext amd64 0.18.1.1-8 [1970 kB]
+Get:28 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main debhelper all 9.20120518 [695 kB]
+Get:29 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main dh-autoreconf all 6 [15.3 kB]
+Get:30 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost1.49-dev amd64 1.49.0-3 [9266 kB]
+Get:31 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost-date-time1.49.0 amd64 1.49.0-3 [46.1 kB]
+Get:32 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost-serialization1.49.0 amd64 1.49.0-3 [209 kB]
+Get:33 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost-serialization1.49-dev amd64 1.49.0-3 [305 kB]
+Get:34 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost-date-time1.49-dev amd64 1.49.0-3 [49.0 kB]
+Get:35 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost-dev amd64 1.49.0.1 [3022 B]
+Get:36 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost-thread1.49.0 amd64 1.49.0-3 [60.5 kB]
+Get:37 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost-thread1.49-dev amd64 1.49.0-3 [65.7 kB]
+Get:38 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libboost-thread-dev amd64 1.49.0.1 [2736 B]
+Get:39 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main zlib1g-dev amd64 1:1.2.7.dfsg-11 [215 kB]
 debconf: delaying package configuration, since apt-utils is not installed
-Fetched 35.7 MB in 2min 33s (233 kB/s)
+Fetched 35.5 MB in 28s (1263 kB/s)
 Selecting previously unselected package libncursesw5:amd64.
-(Reading database ... 11729 files and directories currently installed.)
+(Reading database ... 11778 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) ...
+Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1c-1_amd64.deb) ...
 Selecting previously unselected package libasprintf0c2:amd64.
-Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-7_amd64.deb) ...
+Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-8_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) ...
+Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.12.1-1_amd64.deb) ...
 Selecting previously unselected package libxml2:amd64.
-Unpacking libxml2:amd64 (from .../libxml2_2.7.8.dfsg-9_amd64.deb) ...
+Unpacking libxml2:amd64 (from .../libxml2_2.7.8.dfsg-9.1_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) ...
+Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.32.3-1_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.
@@ -210,11 +182,9 @@ 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) ...
+Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-8_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_9.0.1_amd64.deb) ...
 Selecting previously unselected package groff-base.
 Unpacking groff-base (from .../groff-base_1.21-7_amd64.deb) ...
 Selecting previously unselected package man-db.
@@ -222,7 +192,7 @@ Unpacking man-db (from .../man-db_2.6.1-2_amd64.deb) ...
 Selecting previously unselected package file.
 Unpacking file (from .../archives/file_5.11-1_amd64.deb) ...
 Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-7_amd64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-8_amd64.deb) ...
 Selecting previously unselected package m4.
 Unpacking m4 (from .../archives/m4_1.4.16-3_amd64.deb) ...
 Selecting previously unselected package mime-support.
@@ -244,13 +214,13 @@ Unpacking automake (from .../automake_1%3a1.11.5-1_all.deb) ...
 Selecting previously unselected package html2text.
 Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
 Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-7_amd64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-8_amd64.deb) ...
 Selecting previously unselected package intltool-debian.
 Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
 Selecting previously unselected package po-debconf.
 Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
 Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120419_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120518_all.deb) ...
 Selecting previously unselected package libtool.
 Unpacking libtool (from .../libtool_2.4.2-1_amd64.deb) ...
 Selecting previously unselected package dh-autoreconf.
@@ -276,33 +246,30 @@ Unpacking libboost-thread1.49-dev (from .../libboost-thread1.49-dev_1.49.0-3_amd
 Selecting previously unselected package libboost-thread-dev.
 Unpacking libboost-thread-dev (from .../libboost-thread-dev_1.49.0.1_amd64.deb) ...
 Selecting previously unselected package zlib1g-dev:amd64.
-Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-1_amd64.deb) ...
+Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-11_amd64.deb) ...
 Selecting previously unselected package sbuild-build-depends-cufflinks-dummy.
 Unpacking sbuild-build-depends-cufflinks-dummy (from .../sbuild-build-depends-cufflinks-dummy.deb) ...
 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 libssl1.0.0:amd64 (1.0.1c-1) ...
+Setting up libasprintf0c2:amd64 (0.18.1.1-8) ...
 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 libsqlite3-0:amd64 (3.7.12.1-1) ...
+Setting up libxml2:amd64 (2.7.8.dfsg-9.1) ...
 Setting up libffi5:amd64 (3.0.10-3) ...
-Setting up libglib2.0-0:amd64 (2.32.2-1) ...
+Setting up libglib2.0-0:amd64 (2.32.3-1) ...
 No schema files found: doing nothing.
 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 libgettextpo0:amd64 (0.18.1.1-8) ...
 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 (1.21-7) ...
 Setting up man-db (2.6.1-2) ...
 Building database of manual pages ...
 Setting up file (5.11-1) ...
-Setting up gettext-base (0.18.1.1-7) ...
+Setting up gettext-base (0.18.1.1-8) ...
 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.
@@ -315,10 +282,10 @@ 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 (0.18.1.1-7) ...
+Setting up gettext (0.18.1.1-8) ...
 Setting up intltool-debian (0.35.0+20060710.1) ...
 Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120419) ...
+Setting up debhelper (9.20120518) ...
 Setting up libtool (2.4.2-1) ...
 Setting up dh-autoreconf (6) ...
 Setting up libbam-dev (0.1.18-1) ...
@@ -331,7 +298,7 @@ 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 zlib1g-dev:amd64 (1:1.2.7.dfsg-11) ...
 Setting up sbuild-build-depends-cufflinks-dummy (0.invalid.0) ...
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
@@ -339,8 +306,8 @@ Setting up sbuild-build-depends-cufflinks-dummy (0.invalid.0) ...
 └──────────────────────────────────────────────────────────────────────────────┘
 
 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
+Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.3 g++-4.6_4.6.3-5 g++-4.7_4.7.0-9 gcc-4.6_4.6.3-5 gcc-4.7_4.7.0-9 libc6-dev_2.13-32 libstdc++6_4.7.0-9 libstdc++6-4.6-dev_4.6.3-5 libstdc++6-4.7-dev_4.7.0-9 linux-libc-dev_3.2.18-1
+Package versions: apt_0.9.5 autoconf_2.69-1 automake_1:1.11.5-1 autotools-dev_20120210.1 base-files_6.9 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.2 bsdutils_1:2.20.1-5 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_4.7.0-9 dash_0.5.7-3 debconf_1.5.43 debfoster_2.7-1.1 debhelper_9.20120518 debian-archive-keyring_2012.3 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_4.7.0-9 gcc_4:4.7.0-6 gcc-4.6_4.6.3-5 gcc-4.6-base_4.6.3-5 gcc-4.7_4.7.0-9 gcc-4.7-base_4.7.0-9 gettext_0.18.1.1-8 gettext-base_0.18.1.1-8 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 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_2.2.51-7 libapt-pkg4.12_0.9.5 libasprintf0c2_0.18.1.1-8 libattr1_1:2.4.46-7 libbam-dev_0.1.18-1 libblkid1_2.20.1-5 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 libdb5.1_5.1.29-4 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_1:4.7.0-9 libgdbm3_1.8.3-10 libgettextpo0_0.18.1.1-8 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-1.1 libgomp1_4.7.0-9 libgpm2_1.20.4-4 libicu48_4.8.1.1-6 libitm1_4.7.0-9 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-5 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 libpng12-0_1.2.49-1 libpod-plainer-perl_1.03-1 libquadmath0_4.7.0-9 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_3.7.12.1-1 libss2_1.42.2-2 libssl1.0.0_1.0.1c-1 libstdc++6_4.7.0-9 libstdc++6-4.6-dev_4.6.3-5 libstdc++6-4.7-dev_4.7.0-9 libswitch-perl_2.16-2 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_2.20.1-5 libxml2_2.7.8.dfsg-9.1 linux-libc-dev_3.2.18-1 login_1:4.1.5-1 lsb-base_4.1+Debian4 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_2.20.1-5 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_0.0.7 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_2.20.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-11 zlib1g-dev_1:1.2.7.dfsg-11
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
 │ Build                                                                        │
@@ -357,6 +324,7 @@ 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
+dpkg-source: info: applying gcc-4.7.patch
 
 Check disc space
 ────────────────
@@ -373,8 +341,8 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
 SCHROOT_COMMAND=env
 SCHROOT_GID=1000
 SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-c0f656a9-be50-4fae-a8c6-6763088b32b6
-SCHROOT_UID=1000
+SCHROOT_SESSION_ID=sid-amd64-sbuild-4f66719b-7332-4727-9026-c91ab1d92a86
+SCHROOT_UID=31051
 SCHROOT_USER=charles
 SHELL=/bin/sh
 TERM=xterm
@@ -541,7 +509,7 @@ 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 4.7.0-7) 4.7.0
+  GCC version:         gcc (Debian 4.7.0-9) 4.7.0
   Host System type:    x86_64-pc-linux-gnu
   Install prefix:      /usr
   Install eprefix:     ${prefix}
@@ -614,36 +582,630 @@ abundances.h:443:27: warning:   'boost::numeric::ublas::matrix<double> Abundance
 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:123:17: warning: variable 'hits_for_node' set but not used [-Wunused-but-set-variable]
-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
+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::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 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]
+In file included from abundances.cpp:11:0:
+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::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 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::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]
+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::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 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::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 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]
+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::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 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]
+In file included from locfit/lffuns.h:214:0,
+                 from locfit/local.h:106,
+                 from locfit/c_plot.c:6:
+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 [-Wmaybe-uninitialized]
+locfit/c_plot.c:361:43: warning: 'ix' may be used uninitialized in this function [-Wmaybe-uninitialized]
+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]
+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 [-Wmaybe-uninitialized]
+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
+locfit/ev_main.c: In function 'dataf':
+locfit/ev_main.c:152:21: warning: 'nv' 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_trian.o `test -f 'locfit/ev_trian.c' || echo './'`locfit/ev_trian.c
+locfit/ev_trian.c: In function 'triang_grow':
+locfit/ev_trian.c:77:13: warning: 'jm' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/ev_trian.c:76:63: warning: 'im' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/ev_trian.c: In function 'triang_descend':
+locfit/ev_trian.c:121:38: warning: 'jm' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/ev_trian.c:121:31: warning: 'im' may be used uninitialized in this function [-Wmaybe-uninitialized]
+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:98:17: warning: 'sd' may be used uninitialized in this function [-Wuninitialized]
+locfit/minmax.c: In function 'mmax':
+locfit/minmax.c:217:8: warning: 'sing' may be used uninitialized in this function [-Wmaybe-uninitialized]
+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]
+locfit/pout.c: In function 'lines3d':
+locfit/pout.c:112:13: warning: '*((void *)&x1+16)' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:180:17: note: '*((void *)&x1+16)' was declared here
+locfit/pout.c:111:13: warning: '*((void *)&x1+8)' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:180:17: note: '*((void *)&x1+8)' was declared here
+locfit/pout.c:110:13: warning: 'x1' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:180:17: note: 'x1' was declared here
+locfit/pout.c: In function 'contour3d':
+locfit/pout.c:111:13: warning: 'x3[1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:221:48: note: 'x3[1]' was declared here
+locfit/pout.c:110:13: warning: 'x3[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:221:48: note: 'x3[0]' was declared here
+locfit/pout.c:111:13: warning: 'x2[1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:221:41: note: 'x2[1]' was declared here
+locfit/pout.c:110:13: warning: 'x2[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:221:41: note: 'x2[0]' was declared here
+locfit/pout.c:111:13: warning: 'x1[1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:221:34: note: 'x1[1]' was declared here
+locfit/pout.c:110:13: warning: 'x1[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:221:34: note: 'x1[0]' was declared here
+locfit/pout.c:111:13: warning: 'x0[1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:221:27: note: 'x0[1]' was declared here
+locfit/pout.c:110:13: warning: 'x0[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/pout.c:221:27: note: 'x0[0]' was declared here
+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:109:24: warning: 'lxdd' may be used uninitialized in this function [-Wmaybe-uninitialized]
+locfit/wdiag.c:109:18: warning: 'lxd' may be used uninitialized in this function [-Wmaybe-uninitialized]
+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::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 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 [-Wmaybe-uninitialized]
+GBase.cpp: In function 'char* Gsubstr(const char*, char*, char*)':
+GBase.cpp:271:29: warning: 'subs' may be used uninitialized in this function [-Wmaybe-uninitialized]
+GBase.cpp: In function 'char* upCase(const char*)':
+GBase.cpp:397:11: warning: 'upstr' may be used uninitialized in this function [-Wmaybe-uninitialized]
+GBase.cpp: In function 'char* loCase(const char*)':
+GBase.cpp:407:11: warning: 'lostr' may be used uninitialized in this function [-Wmaybe-uninitialized]
+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 'GffObj* redundantTranscripts(GffObj&, GffObj&, bool, bool)':
+gff_utils.cpp:189:27: warning: converting 'false' to pointer type 'GffObj*' [-Wconversion-null]
+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::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 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 [-Wmaybe-uninitialized]
+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::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 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::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]
+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::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 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 
 make[3]: Leaving directory `/«PKGBUILDDIR»/src'
-make[2]: *** [all-recursive] Error 1
+make[3]: Entering directory `/«PKGBUILDDIR»'
+make[3]: Leaving directory `/«PKGBUILDDIR»'
 make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[1]: *** [all] Error 2
 make[1]: Leaving directory `/«PKGBUILDDIR»'
-dh_auto_build: make -j1 returned exit code 2
-make: *** [build] Error 2
-dpkg-buildpackage: error: debian/rules build gave error exit status 2
+   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]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
+ fakeroot debian/rules binary
+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'
+ /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'
+ /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]: Leaving directory `/«PKGBUILDDIR»'
+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_1.3.0-2_amd64.deb'.
+make[1]: Leaving directory `/«PKGBUILDDIR»'
+ dpkg-genchanges  >../cufflinks_1.3.0-2_amd64.changes
+dpkg-genchanges: not including original source code in upload
+ dpkg-source --after-build cufflinks-1.3.0
+dpkg-buildpackage: binary and diff upload (original source NOT included)
 ────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120509-0840
+Build finished at 20120524-1247
 
 Finished
 ────────
 
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes                                                                      │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+cufflinks_1.3.0-2_amd64.changes:
+────────────────────────────────
+
+Format: 1.8
+Date: Thu, 24 May 2012 12:36:16 +0900
+Source: cufflinks
+Binary: cufflinks
+Architecture: source amd64
+Version: 1.3.0-2
+Distribution: unstable
+Urgency: low
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
+Description: 
+ cufflinks  - Transcript assembly, differential expression and regulation for R
+Closes: 672744
+Changes: 
+ cufflinks (1.3.0-2) unstable; urgency=low
+ .
+   [ Charles Plessy ]
+   * Normalised and summarised debian/copyright.
+ .
+   [ Carlos Borroto ]
+   * Added tophat to Enhances
+ .
+   [ Andreas Tille ]
+   * debian/upstream: Added references as specified in tasks file
+   * debian/copyright: Added Upstream-Contact e-mail
+   * debian/patches/gcc-4.7.patch: Fix gcc-4.7 build issue
+     Closes: #672744
+Checksums-Sha1: 
+ ff6334b374c1cd3b63f0f66e449d6e9c20c55c51 1295 cufflinks_1.3.0-2.dsc
+ 08c909b4f179977b620dc9037e0e9fd610ef653a 12997 cufflinks_1.3.0-2.debian.tar.gz
+ a787cff4ebebecd73e50c4112853b6ec76d30350 1042604 cufflinks_1.3.0-2_amd64.deb
+Checksums-Sha256: 
+ 30348e54894451332454a8aa6713c0ca8a18a7c489aacb0b7e9bf515d8f202cb 1295 cufflinks_1.3.0-2.dsc
+ 1bb5d58a1eaeacecf56a36955ee35436a941a8e4234af079ac5e9be91802b4e4 12997 cufflinks_1.3.0-2.debian.tar.gz
+ e45ea2a2f517d558d9540ce75ed72c4c85035a027d9c4a00abe27d78586a6c60 1042604 cufflinks_1.3.0-2_amd64.deb
+Files: 
+ f0aee85490c73460f1eb4b91d0b59bb9 1295 non-free/science optional cufflinks_1.3.0-2.dsc
+ 272aa1a9e3ae79935641e3cb45c2ec3c 12997 non-free/science optional cufflinks_1.3.0-2.debian.tar.gz
+ b4ea215faae024f44c6d5b2d9186c4a7 1042604 non-free/science optional cufflinks_1.3.0-2_amd64.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents                                                             │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+cufflinks_1.3.0-2_amd64.deb
+───────────────────────────
+
+ new debian package, version 2.0.
+ size 1042604 bytes: control archive=1207 bytes.
+     882 bytes,    17 lines      control              
+    1123 bytes,    18 lines      md5sums              
+ Package: cufflinks
+ Version: 1.3.0-2
+ Architecture: amd64
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 5831
+ Pre-Depends: dpkg (>= 1.15.6)
+ Depends: libboost-thread1.49.0 (>= 1.49.0-1), libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.3.3), python (>= 2.6.6-3~)
+ Enhances: tophat
+ 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 2012-05-24 12:47 ./
+drwxr-xr-x root/root         0 2012-05-24 12:47 ./usr/
+drwxr-xr-x root/root         0 2012-05-24 12:47 ./usr/bin/
+-rwxr-xr-x root/root   1654016 2012-05-24 12:47 ./usr/bin/cufflinks
+-rwxr-xr-x root/root     19134 2012-05-24 12:47 ./usr/bin/cuffmerge
+-rwxr-xr-x root/root   1052960 2012-05-24 12:47 ./usr/bin/compress_gtf
+-rwxr-xr-x root/root   1044832 2012-05-24 12:47 ./usr/bin/gtf_to_sam
+-rwxr-xr-x root/root   1547424 2012-05-24 12:47 ./usr/bin/cuffdiff
+-rwxr-xr-x root/root    352656 2012-05-24 12:47 ./usr/bin/cuffcompare
+-rwxr-xr-x root/root    240824 2012-05-24 12:47 ./usr/bin/gffread
+drwxr-xr-x root/root         0 2012-05-24 12:47 ./usr/share/
+drwxr-xr-x root/root         0 2012-05-24 12:47 ./usr/share/man/
+drwxr-xr-x root/root         0 2012-05-24 12:47 ./usr/share/man/man1/
+-rw-r--r-- root/root      1143 2012-05-24 12:47 ./usr/share/man/man1/cuffcompare.1.gz
+-rw-r--r-- root/root      1266 2012-05-24 12:47 ./usr/share/man/man1/cuffdiff.1.gz
+-rw-r--r-- root/root       339 2012-05-24 12:47 ./usr/share/man/man1/gtf_to_sam.1.gz
+-rw-r--r-- root/root      1622 2012-05-24 12:47 ./usr/share/man/man1/gffread.1.gz
+-rw-r--r-- root/root       396 2012-05-24 12:47 ./usr/share/man/man1/compress_gtf.1.gz
+-rw-r--r-- root/root       658 2012-05-24 12:47 ./usr/share/man/man1/cuffmerge.1.gz
+-rw-r--r-- root/root      1718 2012-05-24 12:47 ./usr/share/man/man1/cufflinks.1.gz
+drwxr-xr-x root/root         0 2012-05-24 12:47 ./usr/share/doc/
+drwxr-xr-x root/root         0 2012-05-24 12:47 ./usr/share/doc/cufflinks/
+-rw-r--r-- root/root       779 2011-06-03 11:19 ./usr/share/doc/cufflinks/AUTHORS
+-rw-r--r-- root/root      8825 2012-05-09 09:34 ./usr/share/doc/cufflinks/copyright
+-rw-r--r-- root/root      3536 2011-06-03 11:19 ./usr/share/doc/cufflinks/README
+-rw-r--r-- root/root      1095 2012-05-24 12:36 ./usr/share/doc/cufflinks/changelog.Debian.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build                                                                   │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+lintian
+───────
+
+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.
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
 │ Cleanup                                                                      │
@@ -657,18 +1219,18 @@ Not cleaning session: cloned chroot in use
 └──────────────────────────────────────────────────────────────────────────────┘
 
 Architecture: amd64
-Build-Space: 14932
-Build-Time: 62
+Build-Space: 236272
+Build-Time: 197
 Distribution: unstable
-Fail-Stage: build
-Install-Time: 168
+Install-Time: 37
 Job: cufflinks_1.3.0-2.dsc
+Lintian: pass
 Package: cufflinks
-Package-Time: 257
+Package-Time: 240
 Source-Version: 1.3.0-2
-Space: 14932
-Status: attempted
+Space: 236272
+Status: successful
 Version: 1.3.0-2
 ────────────────────────────────────────────────────────────────────────────────
-Finished at 20120509-0840
-Build needed 00:04:17, 14932k disc space
+Finished at 20120524-1247
+Build needed 00:04:00, 236272k disc space
diff --git a/upload b/upload
index 87bb4e0..d5e7b49 100644
--- a/upload
+++ b/upload
@@ -1,6 +1,5 @@
-u cufflinks_1.3.0-1.dsc ftp.upload.debian.org Fri Jan  6 09:34:52 2012
-u cufflinks_1.3.0-1.debian.tar.gz ftp.upload.debian.org Fri Jan  6 09:34:54 2012
-u cufflinks_1.3.0-1_amd64.deb ftp.upload.debian.org Fri Jan  6 09:34:57 2012
-u cufflinks_1.3.0.orig.tar.gz ftp.upload.debian.org Fri Jan  6 09:35:00 2012
-u cufflinks_1.3.0-1_amd64.changes ftp.upload.debian.org Fri Jan  6 09:35:01 2012
-s cufflinks_1.3.0-1_amd64.changes ftp.upload.debian.org Fri Jan  6 09:35:01 2012
+u cufflinks_1.3.0-2_amd64.deb ftp.upload.debian.org Thu May 24 12:51:23 2012
+u cufflinks_1.3.0-2.dsc ftp.upload.debian.org Thu May 24 12:51:24 2012
+u cufflinks_1.3.0-2.debian.tar.gz ftp.upload.debian.org Thu May 24 12:51:25 2012
+u cufflinks_1.3.0-2_amd64.changes ftp.upload.debian.org Thu May 24 12:51:26 2012
+s cufflinks_1.3.0-2_amd64.changes ftp.upload.debian.org Thu May 24 12:51:26 2012

-- 
Transcript assembly, differential expression, and differential regulation for RNA-Seq.

