[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.13.4-1-1-g1803813
Charles Plessy
plessy at debian.org
Thu Nov 3 02:30:18 UTC 2011
The following commit has been merged in the meta branch:
commit 1803813eb75743bf362a9e2d05e2b7ad8f1a393e
Author: Charles Plessy <plessy at debian.org>
Date: Thu Nov 3 11:28:41 2011 +0900
Build logs for bedtools_2.14.1-1_amd64.changes.
diff --git a/amd64.changes b/amd64.changes
index 3dacb52..8b43634 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 11:14:35 +0900
Source: bedtools
Binary: bedtools
Architecture: source amd64
-Version: 2.13.4-1
+Version: 2.14.1-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -14,39 +14,39 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.4-1) unstable; urgency=low
+ bedtools (2.14.1-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [bce732c] New upstream release and new tool, multiBedIntersect.
Checksums-Sha1:
- f726dd0ed96d54e8c7cba259fad2230be201475a 1967 bedtools_2.13.4-1.dsc
- e2b308c7500928fea8e6b550e9ed250cfa307485 915893 bedtools_2.13.4.orig.tar.gz
- adb83a8d51f7d91a0a3aa14c24c0d577a965b551 4231 bedtools_2.13.4-1.debian.tar.gz
- 0c71f765fa8e48496bbdee7d8288cb3a6af3a841 668496 bedtools_2.13.4-1_amd64.deb
+ 56cdd1e7ec2fef03d0436abc0c75ed4b52280b8c 1967 bedtools_2.14.1-1.dsc
+ 2a49fb48c4a84ceb88fe4b9f973f7b32239d9312 921855 bedtools_2.14.1.orig.tar.gz
+ 1f744b6c1d32e2cacea24b067f0561cce09be183 4282 bedtools_2.14.1-1.debian.tar.gz
+ 0704612762b96e9d0e1fef6a1312bf8984957d48 672084 bedtools_2.14.1-1_amd64.deb
Checksums-Sha256:
- 9d87dcd94bb037ef1efe7b104e5a6d6d7fb9d7bc1f918a4a1cf5c9bc9c0456e6 1967 bedtools_2.13.4-1.dsc
- c6d9d1d738551a0aacc87bf0504f6499fcb7dd9395291bc97f7455a30d5e0f8f 915893 bedtools_2.13.4.orig.tar.gz
- 97f36acef05ab088673d28f3cc5f9bbd68139e8ec4f1563e596f9aec6d35cbbe 4231 bedtools_2.13.4-1.debian.tar.gz
- b7f7fb7fa55fc06404be50d84a94f24c9493fd5ea0a07217a5819d66185338dc 668496 bedtools_2.13.4-1_amd64.deb
+ b56dd42bef320ed4749d3d68b37a16db156d22f24d88ee1f774d9c917336e86d 1967 bedtools_2.14.1-1.dsc
+ 2a8b3199ac5ab24e92d57771363a10b40fb943a11d04d92cf511185c819f28df 921855 bedtools_2.14.1.orig.tar.gz
+ 8081aeb790948a33af955dbb9d6bf2fee99b916b15eb94e9503b44f4f4ce1ed2 4282 bedtools_2.14.1-1.debian.tar.gz
+ 050e5c57ecb8b5883e7f73baaeba1a094d2e4708839c6098d2176a34b53ddb64 672084 bedtools_2.14.1-1_amd64.deb
Files:
- dedcb32670ddbc3343714d2817375be5 1967 science optional bedtools_2.13.4-1.dsc
- 47383058bd48fb64da878e85c5eb1a4a 915893 science optional bedtools_2.13.4.orig.tar.gz
- febaea245d6062613e4f4850de7afc4c 4231 science optional bedtools_2.13.4-1.debian.tar.gz
- ced08b5c78f0e9e9bcff457a5fd73ec5 668496 science optional bedtools_2.13.4-1_amd64.deb
+ 7afe8edce6d4a47d74ea75824246f36b 1967 science optional bedtools_2.14.1-1.dsc
+ 0250cd4e2588bfa69be8ed67a703ce17 921855 science optional bedtools_2.14.1.orig.tar.gz
+ 3ea8a26995be82395b2b7cfb4cb6952d 4282 science optional bedtools_2.14.1-1.debian.tar.gz
+ 493db6f9d2d5a9d55a9c13b551e2a1ea 672084 science optional bedtools_2.14.1-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index 4e1f23b..79d471f 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,18 +1,18 @@
sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (amd64) 29 oct. 2011 11:10 ║
+║ bedtools 2.14.1-1 (amd64) 03 nov. 2011 11:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.1-1
+Source Version: 2.14.1-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/bedtools-KGhHdI/bedtools-2.13.4' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/bedtools-KGhHdI' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-d6b476b8-a79d-4281-b5d6-ab3b979ae82a' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/bedtools-z_ThSh/bedtools-2.14.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bedtools-z_ThSh' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-3e540590-7d1c-4243-ba3b-53a07e74d07c' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -37,14 +37,14 @@ Reading state information...
Local sources
─────────────
-bedtools_2.13.4-1.dsc exists in .; copying to chroot
+bedtools_2.14.1-1.dsc exists in .; copying to chroot
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-ACSY4w/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-5E1xJl/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -60,7 +60,7 @@ 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/718 B of archives.
+Need to get 0 B/714 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 ... 10741 files and directories currently installed.)
@@ -68,7 +68,7 @@ Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-du
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-6W80Nl/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-cn0oaO/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
OK
Reading package lists...
@@ -101,7 +101,7 @@ Need to get 0 B/9841 kB of archives.
After this operation, 27.2 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
(Reading database ... 10741 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_amd64.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -144,7 +144,7 @@ Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously unselected package sbuild-build-depends-bedtools-dummy.
Unpacking sbuild-build-depends-bedtools-dummy (from .../sbuild-build-depends-bedtools-dummy.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpipeline1 (1.2.0-4) ...
Setting up libpcre3 (8.12-4) ...
Setting up libglib2.0-0 (2.28.8-1) ...
No schema files found: doing nothing.
@@ -176,8 +176,8 @@ Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-1 gcc-4.6_4.6.2-1 libc6-dev_2.13-21 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-1 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-1 gcc_4:4.6.1-3 gcc-4.6_4.6.2-1 gcc-4.6-base_4.6.2-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb4.7_4.7.25-20 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgmp3c2_2:4.3.2+dfsg-2 libgomp1_4.6.2-1 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-1 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 libc6-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 linux-libc-dev_3.0.0-5
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb4.7_4.7.25-20 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgmp3c2_2:4.3.2+dfsg-2 libgomp1_4.6.2-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-3 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-3 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-3 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-3 ncurses-bin_5.9-3 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -187,10 +187,10 @@ Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (bedtools_2.13.4-1.dsc)
-dpkg-source: info: extracting bedtools in bedtools-2.13.4
-dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
+dpkg-source: warning: extracting unsigned source package (bedtools_2.14.1-1.dsc)
+dpkg-source: info: extracting bedtools in bedtools-2.14.1
+dpkg-source: info: unpacking bedtools_2.14.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -208,7 +208,7 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-d6b476b8-a79d-4281-b5d6-ab3b979ae82a
+SCHROOT_SESSION_ID=sid-amd64-sbuild-3e540590-7d1c-4243-ba3b-53a07e74d07c
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -220,9 +220,9 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
+dpkg-buildpackage: source version 2.14.1-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build bedtools-2.13.4
+ dpkg-source --before-build bedtools-2.14.1
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
test -x debian/rules
@@ -246,14 +246,14 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- dpkg-source -b bedtools-2.13.4
+ dpkg-source -b bedtools-2.14.1
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: patches are not applied, applying them now
dpkg-source: info: applying gzstream.h.patch
-dpkg-source: info: building bedtools using existing ./bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: building bedtools using existing ./bedtools_2.14.1.orig.tar.gz
dpkg-source: warning: ignoring deletion of file src/utils/bedFile/bedFile.h.orig
-dpkg-source: info: building bedtools in bedtools_2.13.4-1.debian.tar.gz
-dpkg-source: info: building bedtools in bedtools_2.13.4-1.dsc
+dpkg-source: info: building bedtools in bedtools_2.14.1-1.debian.tar.gz
+dpkg-source: info: building bedtools in bedtools_2.14.1-1.dsc
debian/rules build
test -x debian/rules
mkdir -p "."
@@ -442,6 +442,13 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
* compiling multiBamCov.cpp
* linking multiBamCov
+- Building in src/multiIntersectBed
+ * compiling multiIntersectBed.cpp
+ * compiling multiIntersectBedMain.cpp
+multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
+compilation terminated.
+make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
@@ -562,14 +569,14 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_amd64.deb'.
- dpkg-genchanges >../bedtools_2.13.4-1_amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.1-1_amd64.deb'.
+ dpkg-genchanges >../bedtools_2.14.1-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.1
dpkg-source: info: unapplying gzstream.h.patch
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-1113
+Build finished at 20111103-1123
Finished
────────
@@ -581,15 +588,15 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_amd64.changes:
+bedtools_2.14.1-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 11:14:35 +0900
Source: bedtools
Binary: bedtools
Architecture: source amd64
-Version: 2.13.4-1
+Version: 2.14.1-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -597,42 +604,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.4-1) unstable; urgency=low
+ bedtools (2.14.1-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [bce732c] New upstream release and new tool, multiBedIntersect.
Checksums-Sha1:
- 64d592928bb7442257ce318c0a75c7f515c28cf8 1081 bedtools_2.13.4-1.dsc
- e2b308c7500928fea8e6b550e9ed250cfa307485 915893 bedtools_2.13.4.orig.tar.gz
- adb83a8d51f7d91a0a3aa14c24c0d577a965b551 4231 bedtools_2.13.4-1.debian.tar.gz
- 0c71f765fa8e48496bbdee7d8288cb3a6af3a841 668496 bedtools_2.13.4-1_amd64.deb
+ 6ac64965adebaa8daf913c7a645fcdbcb31a3796 1081 bedtools_2.14.1-1.dsc
+ 2a49fb48c4a84ceb88fe4b9f973f7b32239d9312 921855 bedtools_2.14.1.orig.tar.gz
+ 1f744b6c1d32e2cacea24b067f0561cce09be183 4282 bedtools_2.14.1-1.debian.tar.gz
+ 0704612762b96e9d0e1fef6a1312bf8984957d48 672084 bedtools_2.14.1-1_amd64.deb
Checksums-Sha256:
- c4a19d19e55060ee205b2c5f53a35d53835d0627711eb5b49a1d58924d7c2242 1081 bedtools_2.13.4-1.dsc
- c6d9d1d738551a0aacc87bf0504f6499fcb7dd9395291bc97f7455a30d5e0f8f 915893 bedtools_2.13.4.orig.tar.gz
- 97f36acef05ab088673d28f3cc5f9bbd68139e8ec4f1563e596f9aec6d35cbbe 4231 bedtools_2.13.4-1.debian.tar.gz
- b7f7fb7fa55fc06404be50d84a94f24c9493fd5ea0a07217a5819d66185338dc 668496 bedtools_2.13.4-1_amd64.deb
+ b2b11b1ca1973648d8b45261792e38218a3ee19dc318b39d308acfc83caceb96 1081 bedtools_2.14.1-1.dsc
+ 2a8b3199ac5ab24e92d57771363a10b40fb943a11d04d92cf511185c819f28df 921855 bedtools_2.14.1.orig.tar.gz
+ 8081aeb790948a33af955dbb9d6bf2fee99b916b15eb94e9503b44f4f4ce1ed2 4282 bedtools_2.14.1-1.debian.tar.gz
+ 050e5c57ecb8b5883e7f73baaeba1a094d2e4708839c6098d2176a34b53ddb64 672084 bedtools_2.14.1-1_amd64.deb
Files:
- c90f97a54cdb0a8407f4d949b6629b2f 1081 science optional bedtools_2.13.4-1.dsc
- 47383058bd48fb64da878e85c5eb1a4a 915893 science optional bedtools_2.13.4.orig.tar.gz
- febaea245d6062613e4f4850de7afc4c 4231 science optional bedtools_2.13.4-1.debian.tar.gz
- ced08b5c78f0e9e9bcff457a5fd73ec5 668496 science optional bedtools_2.13.4-1_amd64.deb
+ c42dd1b3c10ed0838ef4cd443de79760 1081 science optional bedtools_2.14.1-1.dsc
+ 0250cd4e2588bfa69be8ed67a703ce17 921855 science optional bedtools_2.14.1.orig.tar.gz
+ 3ea8a26995be82395b2b7cfb4cb6952d 4282 science optional bedtools_2.14.1-1.debian.tar.gz
+ 493db6f9d2d5a9d55a9c13b551e2a1ea 672084 science optional bedtools_2.14.1-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_amd64.deb
+bedtools_2.14.1-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 668496 bytes: control archive= 1739 bytes.
+ size 672084 bytes: control archive= 1731 bytes.
865 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.1-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4692
+ Installed-Size: 4695
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -648,49 +655,49 @@ bedtools_2.13.4-1_amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 11:13 ./
-drwxr-xr-x root/root 0 2011-10-29 11:13 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 11:13 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 11:13 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 11:10 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-10-26 20:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-10-26 20:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 20:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-10-26 20:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-10-29 11:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 11:13 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-10-26 20:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-29 10:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11515 2011-10-26 20:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 584 2011-10-29 11:09 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-29 11:13 ./usr/bin/
--rwxr-xr-x root/root 147112 2011-10-29 11:13 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 179880 2011-10-29 11:13 ./usr/bin/pairToPair
--rwxr-xr-x root/root 276376 2011-10-29 11:13 ./usr/bin/coverageBed
--rwxr-xr-x root/root 229232 2011-10-29 11:13 ./usr/bin/bedToBam
--rwxr-xr-x root/root 93664 2011-10-29 11:13 ./usr/bin/overlap
--rwxr-xr-x root/root 110064 2011-10-29 11:13 ./usr/bin/linksBed
--rwxr-xr-x root/root 114112 2011-10-29 11:13 ./usr/bin/mergeBed
--rwxr-xr-x root/root 114168 2011-10-29 11:13 ./usr/bin/complementBed
--rwxr-xr-x root/root 147136 2011-10-29 11:13 ./usr/bin/nucBed
--rwxr-xr-x root/root 118736 2011-10-29 11:13 ./usr/bin/flankBed
--rwxr-xr-x root/root 267608 2011-10-29 11:13 ./usr/bin/tagBam
--rwxr-xr-x root/root 345456 2011-10-29 11:13 ./usr/bin/intersectBed
--rwxr-xr-x root/root 118328 2011-10-29 11:13 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 110056 2011-10-29 11:13 ./usr/bin/slopBed
--rwxr-xr-x root/root 110000 2011-10-29 11:13 ./usr/bin/annotateBed
--rwxr-xr-x root/root 118192 2011-10-29 11:13 ./usr/bin/subtractBed
--rwxr-xr-x root/root 135200 2011-10-29 11:13 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 278736 2011-10-29 11:13 ./usr/bin/windowBed
--rwxr-xr-x root/root 148424 2011-10-29 11:13 ./usr/bin/sortBed
--rwxr-xr-x root/root 101856 2011-10-29 11:13 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 126464 2011-10-29 11:13 ./usr/bin/closestBed
--rwxr-xr-x root/root 218312 2011-10-29 11:13 ./usr/bin/bamToBed
--rwxr-xr-x root/root 356352 2011-10-29 11:13 ./usr/bin/pairToBed
--rwxr-xr-x root/root 294888 2011-10-29 11:13 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 65032 2011-10-29 11:13 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 126480 2011-10-29 11:13 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 292728 2011-10-29 11:13 ./usr/bin/multiBamCov
+drwxr-xr-x root/root 0 2011-11-03 11:22 ./
+drwxr-xr-x root/root 0 2011-11-03 11:22 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 11:22 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 11:22 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 11:20 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2011-11-03 06:45 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-11-03 06:45 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-03 06:45 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-03 06:45 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-11-03 11:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 11:22 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-03 06:45 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-11-03 11:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11515 2011-11-03 06:45 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 634 2011-11-03 11:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-03 11:22 ./usr/bin/
+-rwxr-xr-x root/root 147112 2011-11-03 11:22 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 180000 2011-11-03 11:22 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 276496 2011-11-03 11:22 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 229232 2011-11-03 11:22 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 93664 2011-11-03 11:22 ./usr/bin/overlap
+-rwxr-xr-x root/root 110184 2011-11-03 11:22 ./usr/bin/linksBed
+-rwxr-xr-x root/root 114112 2011-11-03 11:22 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 114168 2011-11-03 11:22 ./usr/bin/complementBed
+-rwxr-xr-x root/root 147136 2011-11-03 11:22 ./usr/bin/nucBed
+-rwxr-xr-x root/root 118856 2011-11-03 11:22 ./usr/bin/flankBed
+-rwxr-xr-x root/root 267728 2011-11-03 11:22 ./usr/bin/tagBam
+-rwxr-xr-x root/root 345576 2011-11-03 11:22 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 118328 2011-11-03 11:22 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 110136 2011-11-03 11:22 ./usr/bin/slopBed
+-rwxr-xr-x root/root 110000 2011-11-03 11:22 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 118192 2011-11-03 11:22 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 135320 2011-11-03 11:22 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 278856 2011-11-03 11:22 ./usr/bin/windowBed
+-rwxr-xr-x root/root 150952 2011-11-03 11:22 ./usr/bin/sortBed
+-rwxr-xr-x root/root 101856 2011-11-03 11:22 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 126592 2011-11-03 11:22 ./usr/bin/closestBed
+-rwxr-xr-x root/root 218312 2011-11-03 11:22 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 356352 2011-11-03 11:22 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 294888 2011-11-03 11:22 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 65032 2011-11-03 11:22 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 126480 2011-11-03 11:22 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 292848 2011-11-03 11:22 ./usr/bin/multiBamCov
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -815,18 +822,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 135504
-Build-Time: 142
+Build-Space: 137012
+Build-Time: 156
Distribution: unstable
-Install-Time: 12
-Job: bedtools_2.13.4-1.dsc
+Install-Time: 11
+Job: bedtools_2.14.1-1.dsc
Lintian: pass
Package: bedtools
-Package-Time: 159
-Source-Version: 2.13.4-1
-Space: 135504
+Package-Time: 172
+Source-Version: 2.14.1-1
+Space: 137012
Status: successful
-Version: 2.13.4-1
+Version: 2.14.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-1113
-Build needed 00:02:39, 135504k disc space
+Finished at 20111103-1123
+Build needed 00:02:52, 137012k disc space
diff --git a/dsc b/dsc
index 40e6248..83c5d2d 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: bedtools
Binary: bedtools
Architecture: any
-Version: 2.13.4-1
+Version: 2.14.1-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>
Dm-Upload-Allowed: yes
@@ -17,29 +17,29 @@ Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
Package-List:
bedtools deb science optional
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+ 2a49fb48c4a84ceb88fe4b9f973f7b32239d9312 921855 bedtools_2.14.1.orig.tar.gz
+ 1f744b6c1d32e2cacea24b067f0561cce09be183 4282 bedtools_2.14.1-1.debian.tar.gz
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--
Suite of utilities for comparing genomic features.
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