[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.13.4-1-4-g53a72c5
Charles Plessy
plessy at debian.org
Sat Nov 5 01:40:55 UTC 2011
The following commit has been merged in the meta branch:
commit 20347e3debe05cb37ae5d8850dccbaf8e4bd90cb
Author: Charles Plessy <plessy at debian.org>
Date: Sat Nov 5 10:36:41 2011 +0900
Collected build logs for 2.14.2-1.
diff --git a/armel.log b/armel.log
index d1dc18c..395e7a0 100644
--- a/armel.log
+++ b/armel.log
@@ -1,43 +1,43 @@
-From buildd at ancina.debian.org Sat Oct 29 03:27:48 2011
+From buildd at ancina.debian.org Thu Nov 03 10:54:18 2011
Return-path: <buildd at ancina.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
- id 1RJzaG-0003iC-8y
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- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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+ id 1RLuw4-0005Xj-UY
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Received: from buildd by ancina.debian.org with local (Exim 4.69)
(envelope-from <buildd at ancina.debian.org>)
- id 1RJzaE-0005bG-Qb; Sat, 29 Oct 2011 03:27:46 +0000
+ id 1RLuvz-0004kF-06; Thu, 03 Nov 2011 10:54:11 +0000
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-Date: Sat, 29 Oct 2011 03:27:46 +0000
+Date: Thu, 3 Nov 2011 10:54:10 +0000
From: Build Daemon <buildd at ancina.debian.org>
To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on armel (dist=sid)
-Key-Id: 534B6930
-Message-Id: <E1RJzaE-0005bG-Qb at ancina.debian.org>
+Subject: Log for successful build of bedtools_2.14.2-1 on armel (dist=sid)
+Key-Id: 82E89EDA
+Message-Id: <E1RLuvz-0004kF-06 at ancina.debian.org>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ancina.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (armel) 29 Oct 2011 03:05 ║
+║ bedtools 2.14.2-1 (armel) 03 Nov 2011 10:31 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: armel
Hit http://ftp.de.debian.org sid InRelease
Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
@@ -48,20 +48,19 @@ Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
Ign http://ftp.de.debian.org sid/contrib TranslationIndex
Hit http://ftp.de.debian.org sid/main TranslationIndex
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Ign http://ftp.de.debian.org sid/contrib Translation-en
+Hit http://incoming.debian.org Release.gpg
Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/main armel Packages/DiffIndex
+Ign http://ftp.de.debian.org sid/contrib Translation-en
Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Get:3 http://incoming.debian.org Sources [36.2 kB]
-Get:4 http://incoming.debian.org Packages [324 kB]
+Hit http://incoming.debian.org Release
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 362 kB in 10s (35.2 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +81,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 1s (626 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 0s (1202 kB/s)
Download complete and in download only mode
Check arch
@@ -106,12 +105,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -166,11 +165,11 @@ Recommended packages:
autotools-dev
The following NEW packages will be installed:
cdbs diffstat quilt
-0 upgraded, 3 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 3 newly installed, 0 to remove and 14 not upgraded.
Need to get 0 B/461 kB of archives.
After this operation, 1215 kB of additional disk space will be used.
Selecting previously unselected package cdbs.
-(Reading database ... 23123 files and directories currently installed.)
+(Reading database ... 23122 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
@@ -184,11 +183,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.31-rc9 armel (armv5tel)
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: apex-nslu2_1.6.10 apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 bc_1.06.95-2 bf-utf-source_0.05-0.1 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 ca-certificates_20111022 cdbs_0.4.99 cmake_2.8.5-1 cmake-data_2.8.5-1 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-1 cramfsprogs_1.1-6 dash_0.5.7-2 dctrl-tools_2.19 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debiandoc-sgml_1.2.25 debianutils_4.0.4 devio_1.2-1+b1 diffstat_1.54-1 diffutils_1:3.2-1 dmsetup_2:1.02.67-1 dns323-firmware-tools_0.3-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 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 emacsen-common_1.4.22 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.2-1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-1 gcc-4.6-base_4.6.2-1 generatorrunner_0.6.14-2 genext2fs_1.4.1-3 genisoimage_9:1.1.11-2 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 libapiextractor-dev_0.10.8-1 libapiextractor0.10_0.10.8-1 libarchive1_2.8.5-3+b1 libattr1_1:2.4.46-3 libaudio2_1.9.3-1 libblkid1_2.19.1-5 libbogl-dev_0.1.18-5 libbogl0_0.1.18-5 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 libc6-pic_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libcurl3_7.21.7-3 libcurl3-gnutls_7.21.7-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 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+Package versions: apex-nslu2_1.6.10 apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 bc_1.06.95-2 bf-utf-source_0.05-0.1 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 ca-certificates_20111022 cdbs_0.4.99 cmake_2.8.5-1 cmake-data_2.8.5-1 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-1 cramfsprogs_1.1-6 dash_0.5.7-2 dctrl-tools_2.19 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debiandoc-sgml_1.2.25 debianutils_4.0.4 devio_1.2-1+b1 diffstat_1.54-1 diffutils_1:3.2-1 dmsetup_2:1.02.67-1 dns323-firmware-tools_0.3-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 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 emacsen-common_1.4.22 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.2-1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-1 gcc-4.6-base_4.6.2-1 generatorrunner_0.6.14-2 genext2fs_1.4.1-3 genisoimage_9:1.1.11-2 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 libapiextractor-dev_0.10.8-1 libapiextractor0.10_0.10.8-1 libarchive1_2.8.5-3+b1 libattr1_1:2.4.46-3 libaudio2_1.9.3-1 libblkid1_2.19.1-5 libbogl-dev_0.1.18-5 libbogl0_0.1.18-5 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 libc6-pic_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libcurl3_7.21.7-3 libcurl3-gnutls_7.21.7-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 libgcrypt11_1.5.0-3 libgd2-noxpm_2.0.36~rc1~dfsg-6 libgdbm3_1.8.3-10 libgenrunner-dev_0.6.14-2 libgenrunner0.6_0.6.14-2 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.11-1 libgomp1_4.6.2-1 libgpg-error0_1.10-1 libgpm2_1.20.4-4 libgssapi-krb5-2_1.9.1+dfsg-3 libhtml-parser-perl_3.69-1 libhtml-tagset-perl_3.20-2 libice6_2:1.0.7-2 libidn11_1.22-3 libjpeg8_8c-2 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblcms1_1.19.dfsg-1+b1 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libnewt-dev_0.52.11-2.1 libnewt-pic_0.52.11-2.1 libnewt0.52_0.52.11-2.1 libp11-kit0_0.8-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpython2.6_2.6.7-4 libpython2.7_2.7.2-7 libqt4-dbus_4:4.7.3-8 libqt4-declarative_4:4.7.3-8 libqt4-designer_4:4.7.3-8 libqt4-dev_4:4.7.3-8 libqt4-help_4:4.7.3-8 libqt4-network_4:4.7.3-8 libqt4-qt3support_4:4.7.3-8 libqt4-script_4:4.7.3-8 libqt4-scripttools_4:4.7.3-8 libqt4-sql_4:4.7.3-8 libqt4-svg_4:4.7.3-8 libqt4-test_4:4.7.3-8 libqt4-xml_4:4.7.3-8 libqt4-xmlpatterns_4:4.7.3-8 libqtcore4_4:4.7.3-8 libqtgui4_4:4.7.3-8 libreadline5_5.2-11 libreadline6_6.2-7 libroman-perl_1.23-1 librtmp0_2.4~20110711.gitc28f1bab-1 libruby1.8_1.8.7.352-2 libsasl2-2_2.1.25.dfsg1-2 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libsgmls-perl_1.03ii-32 libsigsegv2_2.9-4 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libslang2-pic_2.2.4-3 libsm6_2:1.2.0-2 libsp1c2_1.3.4-1.2.1-47.1 libsparsehash-dev_1.10-1 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-10-16-1 libssh2-1_1.2.8-2 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libtasn1-3_2.10-1 libtext-format-perl_0.53-1 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libudev0_172-1 libunistring0_0.9.3-4 liburi-perl_1.59-1 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libvolume-id1_0.141-2 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libxau6_1:1.0.6-3 libxcb1_1.7-3 libxdmcp6_1:1.1.0-3 libxext6_2:1.3.0-3 libxml2_2.7.8.dfsg-5 libxmlrpc-core-c3_1.16.33-3.1 libxrender1_1:0.9.6-2 libxslt1.1_1.1.26-8 libxt6_1:1.1.1-2 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 mime-support_3.51-1 mklibs_0.1.33 mklibs-copy_0.1.33 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 nullmailer_1:1.05-1 openssl_1.0.0e-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 procps_1:3.2.8-11 psmisc_22.14-1 python_2.7.2-9 python-all_2.7.2-9 python-all-dbg_2.7.2-9 python-all-dev_2.7.2-9 python-dbg_2.7.2-9 python-dev_2.7.2-9 python-minimal_2.7.2-9 python2.6_2.6.7-4 python2.6-dbg_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.2-7 python2.7-dbg_2.7.2-7 python2.7-dev_2.7.2-7 python2.7-minimal_2.7.2-7 qt4-linguist-tools_4:4.7.3-8 qt4-qmake_4:4.7.3-8 quilt_0.48-8 readline-common_6.2-7 ruby1.8_1.8.7.352-2 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sgmlspl_1.03ii-32 slugimage_1:0.0+r104-5 sp_1.3.4-1.2.1-47.1 sudo_1.8.3-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 ttf-dejavu-core_2.33-2 tzdata_2011n-1 u-boot-tools_2011.09-1 uboot-mkimage_2011.09-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 wget_1.13.4-1 x11-common_1:7.6+9 xml-core_0.13 xsltproc_1.1.26-8 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 │
@@ -199,12 +198,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -215,24 +214,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -245,21 +244,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -431,6 +430,13 @@ 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
@@ -506,7 +512,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -578,22 +584,22 @@ dpkg-shlibdeps: warning: debian/bedtools/usr/bin/complementBed contains an unres
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bedtools_2.13.4-1_armel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bedtools_2.14.2-1_armel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0327
+Build finished at 20111103-1053
-bedtools_2.13.4-1_armel.changes:
+bedtools_2.14.2-1_armel.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: armel
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
Maintainer: armel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org>
@@ -601,30 +607,30 @@ 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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- 9f3ddd65de23e3d9f429aeed4acf58dbe9d74006 536930 bedtools_2.13.4-1_armel.deb
+ cf11195f48310815e6789aa682caaf14b6a2dda8 539074 bedtools_2.14.2-1_armel.deb
Checksums-Sha256:
- 1fc8440979c587c0331388d62f020c01e7da0684cb06e2226f32da365d43a988 536930 bedtools_2.13.4-1_armel.deb
+ c8756bb902e813a1c124e9514ede1cbdc21dd7747c6bfd5b8f000474594c2628 539074 bedtools_2.14.2-1_armel.deb
Files:
- cbe86889ba6a8d9ca338addb04f4bc70 536930 science optional bedtools_2.13.4-1_armel.deb
+ 33f2a427cfc41a17b6888b9ab33a8cf7 539074 science optional bedtools_2.14.2-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_armel.deb
+bedtools_2.14.2-1_armel.deb
───────────────────────────
new debian package, version 2.0.
- size 536930 bytes: control archive= 1729 bytes.
+ size 539074 bytes: control archive= 1725 bytes.
865 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 3948
@@ -643,7 +649,7 @@ bedtools_2.13.4-1_armel.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-armel-sbuild-e9c05b69-e231-4b61-a0b6-46d1571b58ec/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools_2.13.4-1_armel.deb' contains ununderstood data member data.tar.xz , giving up
+dpkg-deb: file `/var/lib/schroot/mount/sid-armel-sbuild-e3368794-2dfc-42e0-8818-e90a3e152634/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools_2.14.2-1_armel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -657,19 +663,19 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-e9c05b69-e231-4b61-a0b6-46d1571b58ec/build/buildd-bedtools_2.13.4-1-armel-YeGMVB
+Purging /var/lib/schroot/mount/sid-armel-sbuild-e3368794-2dfc-42e0-8818-e90a3e152634/build/buildd-bedtools_2.14.2-1-armel-rFTHtU
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
cdbs* diffstat* quilt*
-0 upgraded, 0 newly installed, 3 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 3 to remove and 14 not upgraded.
After this operation, 1215 kB disk space will be freed.
-(Reading database ... 23257 files and directories currently installed.)
+(Reading database ... 23256 files and directories currently installed.)
Removing cdbs ...
Removing quilt ...
Purging configuration files for quilt ...
@@ -681,18 +687,18 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 97844
-Build-Time: 1247
+Build-Space: 98536
+Build-Time: 1288
Distribution: sid
-Install-Time: 29
-Job: bedtools_2.13.4-1
+Install-Time: 26
+Job: bedtools_2.14.2-1
Package: bedtools
-Package-Time: 1312
-Source-Version: 2.13.4-1
-Space: 97844
+Package-Time: 1344
+Source-Version: 2.14.2-1
+Space: 98536
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0327
-Build needed 00:21:52, 97844k disc space
-Signature with key '534B6930' requested:
+Finished at 20111103-1053
+Build needed 00:22:24, 98536k disc space
+Signature with key '82E89EDA' requested:
diff --git a/hurd-i386.log b/hurd-i386.log
index a3e5029..78fc3c8 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,83 +1,74 @@
-From buildd at bach.debian.net Sat Oct 29 03:17:08 2011
-Return-path: <buildd at bach.debian.net>
-Received: from callisto.debian.net ([80.87.129.151])
+From buildd at rossini.debian.net Thu Nov 03 04:07:06 2011
+Return-path: <buildd at rossini.debian.net>
+Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at bach.debian.net>)
- id 1RJzPv-0002AA-LE
- for logs at buildd.debian.org; Sat, 29 Oct 2011 03:17:08 +0000
-Received: from bach.debian.net ([10.3.0.1])
- by callisto.debian.net with esmtp (Exim 4.69)
- (envelope-from <buildd at bach.debian.net>)
- id 1RJzPr-0004eT-Fo; Sat, 29 Oct 2011 04:17:03 +0100
-Received: from buildd by bach.debian.net with local (Exim 4.72)
- (envelope-from <buildd at bach.debian.net>)
- id 1RJzPt-00079l-Fw; Sat, 29 Oct 2011 03:17:05 +0000
-Date: Sat, 29 Oct 2011 03:17:05 +0000
-Message-Id: <E1RJzPt-00079l-Fw at bach.debian.net>
-From: Build Daemon <buildd at bach.debian.net>
+ (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
+ id 1RLoZy-0005x0-Og
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:07:06 +0000
+Received: from hurd.ethz.ch ([192.33.98.55] helo=rossini.debian.net)
+ by io.debian.net with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
+ id 1RLoZt-0002zC-UU; Thu, 03 Nov 2011 05:06:58 +0100
+Received: from buildd by rossini.debian.net with local (Exim 4.72)
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+ id 1RLoZs-0000HZ-G6; Thu, 03 Nov 2011 04:06:56 +0000
+Date: Thu, 03 Nov 2011 04:06:56 +0000
+Message-Id: <E1RLoZs-0000HZ-G6 at rossini.debian.net>
+From: Build Daemon <buildd at rossini.debian.net>
To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on hurd-i386
- (dist=unstable)
+Subject: Log for successful build of bedtools_2.14.2-1 on hurd-i386 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on bach.debian.net
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rossini.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (hurd-i386) 29 oct. 2011 03:04 ║
+║ bedtools 2.14.2-1 (hurd-i386) 03 Nov 2011 03:50 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: hurd-i386
-Hit http://ftp.uk.debian.org sid InRelease
-Hit http://ftp.fr.debian.org sid InRelease
+Ign file: ./ InRelease
+Ign file: ./ Release.gpg
+Ign file: ./ Release
+Ign file: ./ Translation-en
+Hit http://ftp.ch.debian.org unstable InRelease
+Hit http://ftp.ch.debian.org experimental InRelease
+Hit http://ftp.fr.debian.org unstable InRelease
+Hit http://ftp.fr.debian.org experimental InRelease
Ign http://incoming.debian.org InRelease
-Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
Ign http://ftp.debian-ports.org unreleased InRelease
Get:1 http://incoming.debian.org Release.gpg [836 B]
-Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
-Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
-Hit http://ftp.uk.debian.org sid/main TranslationIndex
-Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
-Hit http://ftp.fr.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.ch.debian.org unstable/main Sources/DiffIndex
Hit http://ftp.debian-ports.org unreleased Release.gpg
Get:2 http://incoming.debian.org Release [1604 B]
-Hit http://ftp.uk.debian.org sid/main Translation-fr
-Hit http://ftp.fr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex
-Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.fr.debian.org sid/main TranslationIndex
-Ign http://ftp.fr.debian.org sid/non-free TranslationIndex
+Hit http://ftp.ch.debian.org unstable/contrib Sources/DiffIndex
+Hit http://ftp.ch.debian.org unstable/non-free Sources/DiffIndex
+Hit http://ftp.ch.debian.org unstable/main hurd-i386 Packages/DiffIndex
+Hit http://ftp.ch.debian.org unstable/main TranslationIndex
Hit http://ftp.debian-ports.org unreleased Release
-Get:3 http://incoming.debian.org Sources [36.2 kB]
-Hit http://ftp.fr.debian.org sid/main Translation-fr
-Ign http://ftp.uk.debian.org sid/contrib Translation-en
-Ign http://ftp.uk.debian.org sid/contrib Translation-fr
-Ign http://ftp.uk.debian.org sid/non-free Translation-en
-Ign http://ftp.uk.debian.org sid/non-free Translation-fr
+Hit http://ftp.ch.debian.org experimental/main Sources/DiffIndex
+Hit http://ftp.ch.debian.org experimental/contrib Sources/DiffIndex
+Hit http://ftp.ch.debian.org experimental/non-free Sources/DiffIndex
+Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
+Get:3 http://incoming.debian.org Sources [40.9 kB]
+Hit http://ftp.fr.debian.org unstable/contrib Sources/DiffIndex
+Hit http://ftp.fr.debian.org unstable/non-free Sources/DiffIndex
+Get:4 http://incoming.debian.org Packages [602 kB]
+Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
+Hit http://ftp.fr.debian.org unstable/main TranslationIndex
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Get:4 http://incoming.debian.org Packages [324 kB]
+Hit http://ftp.fr.debian.org experimental/main Sources/DiffIndex
+Hit http://ftp.fr.debian.org experimental/contrib Sources/DiffIndex
+Hit http://ftp.fr.debian.org experimental/non-free Sources/DiffIndex
Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Ign http://ftp.fr.debian.org sid/contrib Translation-en
-Ign http://ftp.fr.debian.org sid/contrib Translation-fr
-Ign http://ftp.fr.debian.org sid/non-free Translation-en
-Ign http://ftp.fr.debian.org sid/non-free Translation-fr
Ign http://incoming.debian.org Translation-en
Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Ign http://incoming.debian.org Translation-fr
-Ign http://ftp.debian-ports.org unreleased/main Translation-fr
-Fetched 362 kB in 1min 59s (3030 B/s)
+Fetched 646 kB in 2min 35s (4163 B/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -98,11 +89,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 3s (255 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 6s (152 kB/s)
Download complete and in download only mode
Check arch
@@ -122,12 +113,18 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 68 not upgraded.
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 68 not upgraded.
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -136,69 +133,120 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3+hurd.1)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.2)
+coreutils: already installed (8.13-3)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+dpkg: already installed (1.16.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-1)
+grep: already installed (2.9-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
hurd: already installed (20110519-3)
-ncurses-base: already installed (5.9-1)
+ncurses-base: already installed (5.9-2)
ncurses-bin: already installed (5.9-2)
perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
-sysvinit-utils: already installed (2.88dsf-13.10)
-sysvinit: already installed (2.88dsf-13.10)
-tar: already installed (1.25-2)
-bsdutils: already installed (1:2.16.2-0)
-util-linux: already installed (2.16.2-0)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+util-linux: already installed (2.19.1-5)
libc0.3-dev: already installed (2.13-21)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
hurd-dev: already installed (20110519-3)
cdbs: missing
-debhelper: already installed (8.9.8 >= 8 is satisfied)
+debhelper: missing
+Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- diffstat
+ diffstat file gettext gettext-base html2text intltool-debian libcroco3
+ libexpat1 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
Suggested packages:
- devscripts procmail graphviz
+ devscripts dh-make gettext-doc libmail-box-perl procmail graphviz
Recommended packages:
- autotools-dev
+ autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs diffstat quilt zlib1g-dev
-0 upgraded, 4 newly installed, 0 to remove and 68 not upgraded.
-Need to get 0 B/648 kB of archives.
-After this operation, 1633 kB of additional disk space will be used.
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libcroco3 libexpat1 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
+ quilt zlib1g-dev
+0 upgraded, 17 newly installed, 0 to remove and 22 not upgraded.
+Need to get 0 B/7203 kB of archives.
+After this operation, 20.4 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- cdbs diffstat quilt zlib1g-dev
+ libglib2.0-0 libxml2 libcroco3 libexpat1 libunistring0 libmagic1 file
+ gettext-base cdbs html2text gettext intltool-debian po-debconf debhelper
+ diffstat quilt zlib1g-dev
Authentication warning overridden.
-Selecting previously deselected package cdbs.
-(Reading database ... 14844 files and directories currently installed.)
+Selecting previously unselected package libglib2.0-0.
+(Reading database ... 12467 files and directories currently installed.)
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_hurd-i386.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_hurd-i386.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_hurd-i386.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_hurd-i386.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_hurd-i386.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.09-2_hurd-i386.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../file_5.09-2_hurd-i386.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_hurd-i386.deb) ...
+Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-5_hurd-i386.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
Processing triggers for man-db ...
+Processing triggers for install-info ...
+Setting up libglib2.0-0 (2.28.8-1) ...
+No schema files found: doing nothing.
+Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libcroco3 (0.6.2-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
+Setting up libunistring0 (0.9.3-5) ...
+Setting up libmagic1 (5.09-2) ...
+Setting up file (5.09-2) ...
+Setting up gettext-base (0.18.1.1-5) ...
Setting up cdbs (0.4.99) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up gettext (0.18.1.1-5) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.9.8) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -206,11 +254,14 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 68 not upgraded.
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.1 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 hurd-dev_20110519-3 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.8 apt-utils_0.8.15.8 autopoint_0.18.1.1-4 base-files_6.4 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsd-mailx_8.1.2-0.20100314cvs-1 bsdmainutils_8.2.3 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20110502+nmu1 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-9+hurd.1 cron_3.0pl1-118 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.6-2 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 exim4-base_4.76-2+b3 exim4-config_4.76-2 exim4-daemon-light_4.76-2+b3 fakeroot_1.15.1-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.0-6 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.1-2 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran_4:4.6.0-6 gfortran-4.6_4.6.1-9+hurd.1 git_1:1.7.6.3-1 git-man_1:1.7.6.3-1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.7-3 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 liberror-perl_0.17-1 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.8-1 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libidn11_1.22-3 libldap-2.4-2_2.4.25-3 liblockfile-bin_1.09-3 liblockfile1_1.09-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libp11-kit0_0.7-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-5 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-7 librtmp0_2.4~20110711.gitc28f1bab-1 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libtext-charwidth-perl_0.04-6+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-4 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-2 netbase_4.46 netcat-traditional_1.10-39 openssl_1.0.0e-2 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 quilt_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-2 ttf-bitstream-vera_1.10-8 ttf-freefont_20100919-1 type-handling_0.2.23 tzdata_2011h-3 ucf_3.0025+nmu2 util-linux_2.16.2-0 xml-core_0.13 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.1 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 hurd-dev_20110519-3 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1
+Package versions: adduser_3.113 apt_0.8.15.8 apt-utils_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.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 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.4_4.4.6-11 cpp-4.5_4.5.3-9 cpp-4.6_4.6.1-9+hurd.1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.15.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-11 gcc-4.4-base_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gfortran_4:4.6.1-3 gfortran-4.4_4.4.6-11 gfortran-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-11 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.42.0_1.42.0-4+b3 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 libexpat1_2.0.1-7.2 libfribidi0_0.19.2-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgmpxx4ldbl_2:5.0.2+dfsg-2 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libident_0.22-3 libidn11_1.22-3 libldap-2.4-2_2.4.25-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libnewt0.52_0.52.11-2.1 libobjc2_4.5.3-9 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-7 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-08-10-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 type-handling_0.2.23 tzdata_2011l-1 util-linux_2.19.1-5 wget_1.13-1 whiptail_0.52.11-2.1 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -221,12 +272,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -242,24 +293,24 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-p
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -272,21 +323,21 @@ rm -f debian/stamp-patch*
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -369,11 +420,11 @@ Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t,
Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
-genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
-genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
+genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
+genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
- Building in src/annotateBed
* compiling annotateMain.cpp
@@ -383,15 +434,15 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
* linking annotateBed
- Building in src/bamToBed
+ * compiling bamToBed.cpp
bamToBed.cpp: In function 'int main(int, char**)':
bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- * compiling bamToBed.cpp
* linking bamToBed
- Building in src/bedToBam
+ * compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * compiling bedToBam.cpp
* linking bedToBam
- Building in src/bedToIgv
@@ -462,6 +513,13 @@ 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
@@ -485,13 +543,13 @@ pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-b
* linking pairToBed
- Building in src/pairToPair
+ * compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling pairToPairMain.cpp
+ * compiling pairToPair.cpp
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
- * compiling pairToPair.cpp
* linking pairToPair
- Building in src/shuffleBed
@@ -510,9 +568,9 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
* linking sortBed
- Building in src/subtractBed
+ * compiling subtractMain.cpp
subtractMain.cpp: In function 'int main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling subtractMain.cpp
* compiling subtractBed.cpp
* linking subtractBed
@@ -525,21 +583,21 @@ tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunuse
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
- * compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * compiling unionBedGraphsMain.cpp
* linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
* linking windowBed
- /usr/bin/fakeroot debian/rules binary-arch
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
touch debian/stamp-makefile-build
+ /usr/bin/fakeroot debian/rules binary-arch
DEB_MAKE_CHECK_TARGET unset, not running checks
test -x debian/rules
dh_testroot
@@ -582,56 +640,56 @@ 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_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd.debian.org> >../bedtools_2.13.4-1_hurd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../bedtools_2.14.2-1_hurd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0316
+Build finished at 20111103-0406
-bedtools_2.13.4-1_hurd-i386.changes:
+bedtools_2.14.2-1_hurd-i386.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: hurd-i386
-Version: 2.13.4-1
-Distribution: unstable
+Version: 2.14.2-1
+Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org>
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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- 3e478dd7008cb15ce49f0cf83e9ef66ae21f9e19 683322 bedtools_2.13.4-1_hurd-i386.deb
+ dc6a53d72b587f81b0be5abcadecf3d826d25762 685282 bedtools_2.14.2-1_hurd-i386.deb
Checksums-Sha256:
- 6311af5c57c8063f27409e5ba4c6209bc08d77727d06ae307ba99b78c8a44ce7 683322 bedtools_2.13.4-1_hurd-i386.deb
+ 5150c5992855eec99032e6f24e2d15f1f465b16e349784c56556a4af99c1c84c 685282 bedtools_2.14.2-1_hurd-i386.deb
Files:
- dcefb0c3be1ae1e076048557aabfb4b7 683322 science optional bedtools_2.13.4-1_hurd-i386.deb
+ a9812484c705604e1d0e333bfb4af2b8 685282 science optional bedtools_2.14.2-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_hurd-i386.deb
+bedtools_2.14.2-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 683322 bytes: control archive= 1742 bytes.
+ size 685282 bytes: control archive= 1737 bytes.
869 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4649
+ Installed-Size: 4655
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.3 (>= 2.4), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -647,49 +705,49 @@ bedtools_2.13.4-1_hurd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 03:14 ./
-drwxr-xr-x root/root 0 2011-10-29 03:14 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 03:15 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 03:14 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 03:15 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-29 03:15 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 03:07 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-29 03:15 ./usr/bin/
--rwxr-xr-x root/root 104532 2011-10-29 03:15 ./usr/bin/annotateBed
--rwxr-xr-x root/root 223904 2011-10-29 03:15 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96364 2011-10-29 03:15 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227776 2011-10-29 03:15 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121332 2011-10-29 03:15 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 122588 2011-10-29 03:15 ./usr/bin/closestBed
--rwxr-xr-x root/root 105476 2011-10-29 03:15 ./usr/bin/complementBed
--rwxr-xr-x root/root 285024 2011-10-29 03:15 ./usr/bin/coverageBed
--rwxr-xr-x root/root 142360 2011-10-29 03:15 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 114464 2011-10-29 03:15 ./usr/bin/flankBed
--rwxr-xr-x root/root 301428 2011-10-29 03:15 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 350580 2011-10-29 03:15 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105660 2011-10-29 03:15 ./usr/bin/linksBed
--rwxr-xr-x root/root 109572 2011-10-29 03:15 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 107068 2011-10-29 03:15 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297320 2011-10-29 03:15 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 142468 2011-10-29 03:15 ./usr/bin/nucBed
--rwxr-xr-x root/root 88172 2011-10-29 03:15 ./usr/bin/overlap
--rwxr-xr-x root/root 366976 2011-10-29 03:15 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178292 2011-10-29 03:15 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129588 2011-10-29 03:15 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105348 2011-10-29 03:15 ./usr/bin/slopBed
--rwxr-xr-x root/root 143492 2011-10-29 03:15 ./usr/bin/sortBed
--rwxr-xr-x root/root 113080 2011-10-29 03:15 ./usr/bin/subtractBed
--rwxr-xr-x root/root 272752 2011-10-29 03:15 ./usr/bin/tagBam
--rwxr-xr-x root/root 59976 2011-10-29 03:15 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285032 2011-10-29 03:15 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-11-03 04:04 ./
+drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 03:54 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/bin/
+-rwxr-xr-x root/root 104532 2011-11-03 04:04 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 223904 2011-11-03 04:04 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96364 2011-11-03 04:04 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 228132 2011-11-03 04:04 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121688 2011-11-03 04:04 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 122976 2011-11-03 04:04 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105832 2011-11-03 04:04 ./usr/bin/complementBed
+-rwxr-xr-x root/root 285024 2011-11-03 04:04 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 142684 2011-11-03 04:04 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 114788 2011-11-03 04:04 ./usr/bin/flankBed
+-rwxr-xr-x root/root 301428 2011-11-03 04:04 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 350580 2011-11-03 04:04 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105984 2011-11-03 04:04 ./usr/bin/linksBed
+-rwxr-xr-x root/root 109928 2011-11-03 04:04 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 108636 2011-11-03 04:04 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297452 2011-11-03 04:04 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 142848 2011-11-03 04:04 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88172 2011-11-03 04:04 ./usr/bin/overlap
+-rwxr-xr-x root/root 366976 2011-11-03 04:04 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178292 2011-11-03 04:04 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129976 2011-11-03 04:04 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 105704 2011-11-03 04:04 ./usr/bin/slopBed
+-rwxr-xr-x root/root 143848 2011-11-03 04:04 ./usr/bin/sortBed
+-rwxr-xr-x root/root 113436 2011-11-03 04:04 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 272752 2011-11-03 04:04 ./usr/bin/tagBam
+-rwxr-xr-x root/root 59976 2011-11-03 04:04 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285032 2011-11-03 04:04 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -703,43 +761,72 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /home/buildd/build/chroot-unstable/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T
+Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 68 not upgraded.
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* diffstat* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 4 to remove and 68 not upgraded.
-After this operation, 1633 kB disk space will be freed.
-(Reading database ... 15015 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libcroco3* libexpat1* libglib2.0-0* libmagic1*
+ libunistring0* libxml2* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 17 to remove and 22 not upgraded.
+After this operation, 20.4 MB disk space will be freed.
+(Reading database ... 13441 files and directories currently installed.)
Removing cdbs ...
+Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libexpat1 ...
+Purging configuration files for libexpat1 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
Removing zlib1g-dev ...
Processing triggers for man-db ...
+Processing triggers for install-info ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 94480
-Build-Time: 556
-Distribution: unstable
-Install-Time: 26
-Job: bedtools_2.13.4-1
+Build-Space: 95452
+Build-Time: 718
+Distribution: sid
+Install-Time: 58
+Job: bedtools_2.14.2-1
Package: bedtools
-Package-Time: 742
-Source-Version: 2.13.4-1
-Space: 94480
+Package-Time: 979
+Source-Version: 2.14.2-1
+Space: 95452
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0316
-Build needed 00:12:22, 94480k disc space
+Finished at 20111103-0406
+Build needed 00:16:19, 95452k disc space
diff --git a/i386.log b/i386.log
index e807ad5..41f2126 100644
--- a/i386.log
+++ b/i386.log
@@ -1,4 +1,4 @@
-From buildd at biber.debian.org Sat Oct 29 03:08:51 2011
+From buildd at biber.debian.org Thu Nov 03 03:44:34 2011
Return-path: <buildd at biber.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,63 +6,63 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1RJzHv-0001DR-1j
- for logs at buildd.debian.org; Sat, 29 Oct 2011 03:08:51 +0000
+ id 1RLoEE-0002fd-MP
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 03:44:34 +0000
Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1RJzHu-0007r6-BX; Sat, 29 Oct 2011 03:08:50 +0000
+ id 1RLoED-0002VL-Oe; Thu, 03 Nov 2011 03:44:33 +0000
Received: from buildd by biber.debian.org with local (Exim 4.72)
(envelope-from <buildd at biber.debian.org>)
- id 1RJzHY-0002T7-Py; Sat, 29 Oct 2011 03:08:28 +0000
-Message-Id: <E1RJzHY-0002T7-Py at biber.debian.org>
+ id 1RLoED-0006lz-5A; Thu, 03 Nov 2011 03:44:33 +0000
+Message-Id: <E1RLoED-0006lz-5A at biber.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 29 Oct 2011 03:08:28 +0000
+Date: Thu, 3 Nov 2011 03:44:33 +0000
From: buildd on biber <buildd at biber.debian.org>
To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on i386 (dist=sid)
-Key-Id: E4786BDC
+Subject: Log for successful build of bedtools_2.14.2-1 on i386 (dist=sid)
+Key-Id: C83D412C
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (i386) 29 Oct 2011 03:03 ║
+║ bedtools 2.14.2-1 (i386) 03 Nov 2011 03:40 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: i386
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Get:1 http://ftp.gr.debian.org unstable InRelease [146 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [5889 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:4 http://ftp.gr.debian.org unstable/contrib Sources [56.9 kB]
+Get:5 http://ftp.gr.debian.org unstable/non-free Sources [104 kB]
+Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7821 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [68.2 kB]
+Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
+Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.gr.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org unstable/main Sources [5874 kB]
-Get:4 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:5 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:6 http://incoming.debian.org unstable/main i386 Packages [7815 kB]
-Get:7 http://incoming.debian.org unstable/contrib i386 Packages [67.9 kB]
+Get:9 http://incoming.debian.org Release.gpg [836 B]
+Get:10 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:13 http://incoming.debian.org unstable/main i386 Packages [7820 kB]
+Get:14 http://incoming.debian.org unstable/contrib i386 Packages [68.2 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:8 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:9 http://incoming.debian.org Release [1604 B]
-Get:10 http://incoming.debian.org Sources [36.2 kB]
-Get:11 http://incoming.debian.org Packages [324 kB]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [47.2 kB]
+Get:18 http://incoming.debian.org Packages [605 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Get:12 http://ftp.gr.debian.org unstable InRelease [146 kB]
-Get:13 http://ftp.gr.debian.org unstable/main Sources [5868 kB]
-Get:14 http://ftp.gr.debian.org unstable/contrib Sources [56.5 kB]
-Get:15 http://ftp.gr.debian.org unstable/non-free Sources [104 kB]
-Get:16 http://ftp.gr.debian.org unstable/main i386 Packages [7812 kB]
-Get:17 http://ftp.gr.debian.org unstable/contrib i386 Packages [68.1 kB]
-Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
-Get:18 http://ftp.gr.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.gr.debian.org unstable/contrib Translation-en
-Fetched 28.5 MB in 27s (1043 kB/s)
+Fetched 28.8 MB in 31s (904 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 1s (472 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 2s (425 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +107,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -127,9 +127,9 @@ bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
+diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
@@ -174,10 +174,10 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 16 not upgraded.
Need to get 9694 kB of archives.
After this operation, 27.3 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-3 [37.6 kB]
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-4 [37.6 kB]
Get:2 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-4 [223 kB]
Get:3 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.8-1 [1633 kB]
Get:4 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-5 [882 kB]
@@ -199,10 +199,10 @@ Get:19 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.54-1 [27.7
Get:20 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9694 kB in 21s (445 kB/s)
+Fetched 9694 kB in 0s (9802 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10633 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_i386.deb) ...
+(Reading database ... 10638 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_i386.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -243,7 +243,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.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.
@@ -272,11 +272,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_2.21.90.20111004-2 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_4.6.1-15 dash_0.5.7-2 debconf_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_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-15 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_1.3.3-15 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 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_4.6.2-2 gcc-4.6_4.6.2-2 libc6-dev_2.13-21 libstdc++6_4.6.2-2 libstdc++6-4.6-dev_4.6.2-2 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_4.6.2-2 dash_0.5.7-2 debconf_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_4.6.2-2 gcc_4:4.6.1-3 gcc-4.6_4.6.2-2 gcc-4.6-base_4.6.2-2 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 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-2 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_1.2.0-4 libquadmath0_4.6.2-2 libreadline6_6.2-7 libselinux1_2.1.0-3 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-2 libstdc++6-4.6-dev_4.6.2-2 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,12 +287,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -303,24 +303,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -333,21 +333,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -519,6 +519,13 @@ 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
@@ -594,7 +601,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -639,22 +646,22 @@ 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_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.13.4-1_i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.14.2-1_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0308
+Build finished at 20111103-0344
-bedtools_2.13.4-1_i386.changes:
+bedtools_2.14.2-1_i386.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: i386
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
@@ -662,33 +669,33 @@ 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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- 52cfafd73701e0abd7582a7b03d02ee6b9192e0b 681952 bedtools_2.13.4-1_i386.deb
+ edd41d0a01700b5ff047a82dd5bf70650b346300 682334 bedtools_2.14.2-1_i386.deb
Checksums-Sha256:
- 9555c63da4b13366aa9ac61676b3d2f52e0bf0b2a77aa77a95b1af819999d9ad 681952 bedtools_2.13.4-1_i386.deb
+ 89d0a8f40b651d682757545bf6ca5e9bf662cb83d5de705da997c907179d0307 682334 bedtools_2.14.2-1_i386.deb
Files:
- cd2a8dafb349927a435b85fbf0650e52 681952 science optional bedtools_2.13.4-1_i386.deb
+ 0aea0bd694c0be19d013c9997a322fd6 682334 science optional bedtools_2.14.2-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_i386.deb
+bedtools_2.14.2-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 681952 bytes: control archive= 1728 bytes.
+ size 682334 bytes: control archive= 1733 bytes.
864 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4634
+ Installed-Size: 4643
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
@@ -704,49 +711,49 @@ bedtools_2.13.4-1_i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 03:08 ./
-drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/bin/
--rwxr-xr-x root/root 142064 2011-10-29 03:08 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 59648 2011-10-29 03:08 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 96356 2011-10-29 03:08 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227628 2011-10-29 03:08 ./usr/bin/bedToBam
--rwxr-xr-x root/root 113880 2011-10-29 03:08 ./usr/bin/flankBed
--rwxr-xr-x root/root 142652 2011-10-29 03:08 ./usr/bin/sortBed
--rwxr-xr-x root/root 297312 2011-10-29 03:08 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 105332 2011-10-29 03:08 ./usr/bin/linksBed
--rwxr-xr-x root/root 141980 2011-10-29 03:08 ./usr/bin/nucBed
--rwxr-xr-x root/root 350572 2011-10-29 03:08 ./usr/bin/intersectBed
--rwxr-xr-x root/root 112716 2011-10-29 03:08 ./usr/bin/subtractBed
--rwxr-xr-x root/root 285024 2011-10-29 03:08 ./usr/bin/windowBed
--rwxr-xr-x root/root 109276 2011-10-29 03:08 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 272744 2011-10-29 03:08 ./usr/bin/tagBam
--rwxr-xr-x root/root 129160 2011-10-29 03:08 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 281508 2011-10-29 03:08 ./usr/bin/coverageBed
--rwxr-xr-x root/root 106740 2011-10-29 03:08 ./usr/bin/mergeBed
--rwxr-xr-x root/root 102964 2011-10-29 03:08 ./usr/bin/annotateBed
--rwxr-xr-x root/root 88164 2011-10-29 03:08 ./usr/bin/overlap
--rwxr-xr-x root/root 121664 2011-10-29 03:08 ./usr/bin/closestBed
--rwxr-xr-x root/root 178284 2011-10-29 03:08 ./usr/bin/pairToPair
--rwxr-xr-x root/root 105148 2011-10-29 03:08 ./usr/bin/complementBed
--rwxr-xr-x root/root 223548 2011-10-29 03:08 ./usr/bin/bamToBed
--rwxr-xr-x root/root 298132 2011-10-29 03:08 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 366968 2011-10-29 03:08 ./usr/bin/pairToBed
--rwxr-xr-x root/root 121164 2011-10-29 03:08 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 104988 2011-10-29 03:08 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 03:05 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/bin/
+-rwxr-xr-x root/root 142420 2011-11-03 03:44 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 59648 2011-11-03 03:44 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 96356 2011-11-03 03:44 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227744 2011-11-03 03:44 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 114204 2011-11-03 03:44 ./usr/bin/flankBed
+-rwxr-xr-x root/root 143008 2011-11-03 03:44 ./usr/bin/sortBed
+-rwxr-xr-x root/root 297312 2011-11-03 03:44 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 105688 2011-11-03 03:44 ./usr/bin/linksBed
+-rwxr-xr-x root/root 142360 2011-11-03 03:44 ./usr/bin/nucBed
+-rwxr-xr-x root/root 350572 2011-11-03 03:44 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 112756 2011-11-03 03:44 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 285024 2011-11-03 03:44 ./usr/bin/windowBed
+-rwxr-xr-x root/root 109600 2011-11-03 03:44 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 272744 2011-11-03 03:44 ./usr/bin/tagBam
+-rwxr-xr-x root/root 129456 2011-11-03 03:44 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 281864 2011-11-03 03:44 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 107064 2011-11-03 03:44 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 104524 2011-11-03 03:44 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 88164 2011-11-03 03:44 ./usr/bin/overlap
+-rwxr-xr-x root/root 122020 2011-11-03 03:44 ./usr/bin/closestBed
+-rwxr-xr-x root/root 178284 2011-11-03 03:44 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 105472 2011-11-03 03:44 ./usr/bin/complementBed
+-rwxr-xr-x root/root 223548 2011-11-03 03:44 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 301420 2011-11-03 03:44 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 366968 2011-11-03 03:44 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 121520 2011-11-03 03:44 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 105344 2011-11-03 03:44 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 03:41 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -760,7 +767,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-1cf97047-5a84-4be2-9ed7-799ebad2a5c3/build/buildd-bedtools_2.13.4-1-i386-kdo61W
+Purging /var/lib/schroot/mount/sid-i386-sbuild-c2668e15-cbf5-4daf-b806-fe3c94bb1ee8/build/buildd-bedtools_2.14.2-1-i386-u4h74k
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -768,18 +775,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 94000
-Build-Time: 168
+Build-Space: 94984
+Build-Time: 173
Distribution: sid
-Install-Time: 60
-Job: bedtools_2.13.4-1
+Install-Time: 40
+Job: bedtools_2.14.2-1
Package: bedtools
-Package-Time: 272
-Source-Version: 2.13.4-1
-Space: 94000
+Package-Time: 258
+Source-Version: 2.14.2-1
+Space: 94984
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0308
-Build needed 00:04:32, 94000k disc space
-Signature with key 'E4786BDC' requested:
+Finished at 20111103-0344
+Build needed 00:04:18, 94984k disc space
+Signature with key 'C83D412C' requested:
diff --git a/ia64.log b/ia64.log
index e973ea4..fb4f5c7 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,4 +1,4 @@
-From buildd at mundy.debian.org Sat Oct 29 05:16:53 2011
+From buildd at mundy.debian.org Thu Nov 03 06:50:36 2011
Return-path: <buildd at mundy.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,22 +6,22 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
- id 1RK1Hp-00033I-4W
- for logs at buildd.debian.org; Sat, 29 Oct 2011 05:16:53 +0000
+ id 1RLr8G-0004d7-J3
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 06:50:36 +0000
Received: from mundy.debian.org ([192.25.206.62])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mundy.debian.org, EMAIL=hostmaster at mundy.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
- id 1RK1Hn-0005PA-UV; Sat, 29 Oct 2011 05:16:52 +0000
+ id 1RLr8F-0002SW-4b; Thu, 03 Nov 2011 06:50:35 +0000
Received: from buildd by mundy.debian.org with local (Exim 4.72)
(envelope-from <buildd at mundy.debian.org>)
- id 1RK1Hl-0007TC-EB; Sat, 29 Oct 2011 05:16:49 +0000
-Date: Sat, 29 Oct 2011 05:16:49 +0000
-Message-Id: <E1RK1Hl-0007TC-EB at mundy.debian.org>
+ id 1RLr8C-0005y1-EX; Thu, 03 Nov 2011 06:50:32 +0000
+Date: Thu, 03 Nov 2011 06:50:32 +0000
+Message-Id: <E1RLr8C-0005y1-EX at mundy.debian.org>
From: buildd on mundy <buildd at mundy.debian.org>
To: dannf at master.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on ia64 (dist=sid)
+Subject: Log for successful build of bedtools_2.14.2-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -29,38 +29,38 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mundy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (ia64) 29 Oct 2011 05:05 ║
+║ bedtools 2.14.2-1 (ia64) 03 Nov 2011 06:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: ia64
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Get:1 http://spohr.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://spohr.debian.org unstable/main Sources [5896 kB]
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org Release [1604 B]
-Get:4 http://incoming.debian.org unstable/main Sources [5874 kB]
-Get:5 http://spohr.debian.org unstable InRelease [146 kB]
-Get:6 http://spohr.debian.org unstable/main Sources [5874 kB]
-Get:7 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:8 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:9 http://incoming.debian.org unstable/main ia64 Packages [7508 kB]
-Get:10 http://incoming.debian.org unstable/contrib ia64 Packages [55.7 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:11 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:12 http://incoming.debian.org Sources [37.0 kB]
-Get:13 http://incoming.debian.org Packages [331 kB]
-Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Get:14 http://spohr.debian.org unstable/contrib Sources [56.5 kB]
-Get:15 http://spohr.debian.org unstable/non-free Sources [104 kB]
-Get:16 http://spohr.debian.org unstable/main ia64 Packages [7508 kB]
-Get:17 http://spohr.debian.org unstable/contrib ia64 Packages [55.7 kB]
+Get:4 http://spohr.debian.org unstable/contrib Sources [56.9 kB]
+Get:5 http://incoming.debian.org Release.gpg [836 B]
+Get:6 http://spohr.debian.org unstable/non-free Sources [104 kB]
+Get:7 http://spohr.debian.org unstable/main ia64 Packages [7525 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [55.9 kB]
Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:18 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
+Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
Ign http://spohr.debian.org unstable/contrib Translation-en
-Fetched 27.9 MB in 19s (1433 kB/s)
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [7525 kB]
+Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [55.9 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [38.7 kB]
+Get:18 http://incoming.debian.org Packages [609 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 28.2 MB in 19s (1475 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -81,11 +81,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 1s (860 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 1s (919 kB/s)
Download complete and in download only mode
Check arch
@@ -184,7 +184,7 @@ The following NEW packages will be installed:
0 upgraded, 21 newly installed, 0 to remove and 46 not upgraded.
Need to get 11.4 MB of archives.
After this operation, 38.5 MB of additional disk space will be used.
-Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-3 [47.8 kB]
+Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-4 [46.7 kB]
Get:2 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
Get:3 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.8-1 [1992 kB]
Get:4 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-5 [1177 kB]
@@ -206,10 +206,10 @@ Get:19 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.54-1 [36.9
Get:20 http://spohr.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.4 MB in 28s (403 kB/s)
+Fetched 11.4 MB in 1s (6219 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10538 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_ia64.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_ia64.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -250,7 +250,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.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.
@@ -286,7 +286,7 @@ Use 'apt-get autoremove' to remove them.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6.1-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 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_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 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-13.11 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 libc6.1_2.13-21 libc6.1-dev_2.13-21 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-13 libreadline6_6.2-5 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-4 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_1.3.3-15 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_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-5 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 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_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 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-13.11 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 libc6.1_2.13-21 libc6.1-dev_2.13-21 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-13 libreadline6_6.2-5 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-4 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_1.3.3-15 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_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-5 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -297,12 +297,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -318,24 +318,24 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIF
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS =
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -348,21 +348,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -538,6 +538,13 @@ 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
@@ -613,7 +620,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -659,22 +666,22 @@ dpkg-shlibdeps: warning: dependency on libm.so.6.1 could be avoided if "debian/b
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../bedtools_2.13.4-1_ia64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../bedtools_2.14.2-1_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0516
+Build finished at 20111103-0650
-bedtools_2.13.4-1_ia64.changes:
+bedtools_2.14.2-1_ia64.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: ia64
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org>
@@ -682,33 +689,33 @@ 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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- 4525b15f5c544c46765a435343c520168a04b333 744358 bedtools_2.13.4-1_ia64.deb
+ 8a121c79f061526410dba664211a0cf073923f7d 746882 bedtools_2.14.2-1_ia64.deb
Checksums-Sha256:
- 35d902ba7ff65a7b30a8418cde058b7e67503a2559c51b8782db5e7f0e346d5d 744358 bedtools_2.13.4-1_ia64.deb
+ 95d352509d50774920156e56071c2d402f8d94af280f201e2341a7c424011795 746882 bedtools_2.14.2-1_ia64.deb
Files:
- 22ea6bd90c3943f471b8b04b14b99447 744358 science optional bedtools_2.13.4-1_ia64.deb
+ 4be0fe6148184b114aeec9d2ed876ed1 746882 science optional bedtools_2.14.2-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_ia64.deb
+bedtools_2.14.2-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 744358 bytes: control archive= 1742 bytes.
+ size 746882 bytes: control archive= 1745 bytes.
880 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 9560
+ Installed-Size: 9566
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6.1 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libunwind7, zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -724,49 +731,49 @@ bedtools_2.13.4-1_ia64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 05:16 ./
-drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 05:07 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/bin/
--rwxr-xr-x root/root 463184 2011-10-29 05:16 ./usr/bin/bamToBed
--rwxr-xr-x root/root 178672 2011-10-29 05:16 ./usr/bin/overlap
--rwxr-xr-x root/root 270696 2011-10-29 05:16 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 471856 2011-10-29 05:16 ./usr/bin/bedToBam
--rwxr-xr-x root/root 219880 2011-10-29 05:16 ./usr/bin/complementBed
--rwxr-xr-x root/root 587752 2011-10-29 05:16 ./usr/bin/windowBed
--rwxr-xr-x root/root 217208 2011-10-29 05:16 ./usr/bin/slopBed
--rwxr-xr-x root/root 305760 2011-10-29 05:16 ./usr/bin/sortBed
--rwxr-xr-x root/root 226280 2011-10-29 05:16 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 297768 2011-10-29 05:16 ./usr/bin/nucBed
--rwxr-xr-x root/root 293648 2011-10-29 05:16 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 221064 2011-10-29 05:16 ./usr/bin/mergeBed
--rwxr-xr-x root/root 234968 2011-10-29 05:16 ./usr/bin/subtractBed
--rwxr-xr-x root/root 251952 2011-10-29 05:16 ./usr/bin/closestBed
--rwxr-xr-x root/root 728240 2011-10-29 05:16 ./usr/bin/intersectBed
--rwxr-xr-x root/root 199440 2011-10-29 05:16 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 564992 2011-10-29 05:16 ./usr/bin/tagBam
--rwxr-xr-x root/root 246744 2011-10-29 05:16 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 220280 2011-10-29 05:16 ./usr/bin/linksBed
--rwxr-xr-x root/root 216544 2011-10-29 05:16 ./usr/bin/annotateBed
--rwxr-xr-x root/root 580280 2011-10-29 05:16 ./usr/bin/coverageBed
--rwxr-xr-x root/root 378032 2011-10-29 05:16 ./usr/bin/pairToPair
--rwxr-xr-x root/root 612040 2011-10-29 05:16 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 620624 2011-10-29 05:16 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 120416 2011-10-29 05:16 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 767632 2011-10-29 05:16 ./usr/bin/pairToBed
--rwxr-xr-x root/root 234456 2011-10-29 05:16 ./usr/bin/flankBed
+drwxr-xr-x root/root 0 2011-11-03 06:49 ./
+drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 06:41 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/bin/
+-rwxr-xr-x root/root 463184 2011-11-03 06:49 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 178912 2011-11-03 06:49 ./usr/bin/overlap
+-rwxr-xr-x root/root 270936 2011-11-03 06:49 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 472096 2011-11-03 06:49 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 220104 2011-11-03 06:49 ./usr/bin/complementBed
+-rwxr-xr-x root/root 587992 2011-11-03 06:49 ./usr/bin/windowBed
+-rwxr-xr-x root/root 217448 2011-11-03 06:49 ./usr/bin/slopBed
+-rwxr-xr-x root/root 306000 2011-11-03 06:49 ./usr/bin/sortBed
+-rwxr-xr-x root/root 226504 2011-11-03 06:49 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 297608 2011-11-03 06:49 ./usr/bin/nucBed
+-rwxr-xr-x root/root 293872 2011-11-03 06:49 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 221304 2011-11-03 06:49 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 235192 2011-11-03 06:49 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 251936 2011-11-03 06:49 ./usr/bin/closestBed
+-rwxr-xr-x root/root 728464 2011-11-03 06:49 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 199664 2011-11-03 06:49 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 565216 2011-11-03 06:49 ./usr/bin/tagBam
+-rwxr-xr-x root/root 246984 2011-11-03 06:49 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 220504 2011-11-03 06:49 ./usr/bin/linksBed
+-rwxr-xr-x root/root 216784 2011-11-03 06:49 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 580520 2011-11-03 06:49 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 378256 2011-11-03 06:49 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 612264 2011-11-03 06:49 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 620864 2011-11-03 06:49 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 120416 2011-11-03 06:49 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 767872 2011-11-03 06:49 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 234680 2011-11-03 06:49 ./usr/bin/flankBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -780,7 +787,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-1ae39a2e-4d0c-42e1-a216-bdc745d88862/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-99cf4c72-9adb-4338-9fcb-fd2e1867e020/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -788,19 +795,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 156600
-Build-Time: 543
+Build-Space: 158140
+Build-Time: 559
Distribution: sid
-Install-Time: 84
-Job: bedtools_2.13.4-1
+Install-Time: 64
+Job: bedtools_2.14.2-1
Package: bedtools
Package-Time: 677
-Source-Version: 2.13.4-1
-Space: 156600
+Source-Version: 2.14.2-1
+Space: 158140
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0516
-Build needed 00:11:17, 156600k disc space
+Finished at 20111103-0650
+Build needed 00:11:17, 158140k disc space
Signature with key '96FA48F4' requested:
diff --git a/info b/info
index 3258c06..4f48ea4 100644
--- a/info
+++ b/info
@@ -1,11 +1,11 @@
-i386~1319857731~sid~successful
-powerpc~1319857796~sid~successful
-hurd-i386~1319858228~sid~successful
-kfreebsd-amd64~1319858240~sid~successful
-mips~1319858838~sid~successful
-armel~1319858868~sid~successful
-kfreebsd-i386~1319860896~sid~successful
-mipsel~1319862768~sid~successful
-sparc~1319863353~sid~successful
-s390~1319863708~sid~successful
-ia64~1319865413~sid~successful
+i386~1320291875~sid~successful
+kfreebsd-i386~1320291957~sid~successful
+powerpc~1320292390~sid~successful
+hurd-i386~1320293227~sid~successful
+sparc~1320293519~sid~successful
+kfreebsd-amd64~1320293701~sid~successful
+mips~1320295049~sid~successful
+mipsel~1320295241~sid~successful
+s390~1320295596~sid~successful
+ia64~1320303037~sid~successful
+armel~1320317658~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 0116b63..1e5650a 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,93 +1,76 @@
-From buildd at fano.debian.org Sat Oct 29 03:17:20 2011
+From buildd at fano.debian.org Thu Nov 03 04:15:01 2011
Return-path: <buildd at fano.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1RJzQ7-0002Au-VY
- for logs at buildd.debian.org; Sat, 29 Oct 2011 03:17:20 +0000
+ id 1RLohg-0006xW-VO
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:15:01 +0000
Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1RJzQ6-0008RR-QB; Sat, 29 Oct 2011 03:17:19 +0000
+ id 1RLohf-0007dP-8H; Thu, 03 Nov 2011 04:15:00 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1RJzQ4-00097p-43; Sat, 29 Oct 2011 03:17:16 +0000
-Message-Id: <E1RJzQ4-00097p-43 at fano.debian.org>
+ id 1RLohc-0007bq-Cq; Thu, 03 Nov 2011 04:14:56 +0000
+Message-Id: <E1RLohc-0007bq-Cq at fano.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 29 Oct 2011 03:17:16 +0000
+Date: Thu, 3 Nov 2011 04:14:56 +0000
From: buildd on fano <buildd at fano.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on kfreebsd-amd64
+Subject: Log for successful build of bedtools_2.14.2-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: 911EAB69
+Key-Id: D33FE1D8
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (kfreebsd-amd64) 29 Oct 2011 03:12 ║
+║ bedtools 2.14.2-1 (kfreebsd-amd64) 03 Nov 2011 04:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: kfreebsd-amd64
-Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Hit http://mirror-ubc.debian.org sid InRelease
+Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:4 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:5 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
-Get:6 http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex [2023 B]
-Get:7 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex [2023 B]
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:8 http://incoming.debian.org sid/main TranslationIndex [2045 B]
-Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:9 http://mirror-ubc.debian.org sid InRelease [146 kB]
-Get:10 http://incoming.debian.org Release [1604 B]
-Get:11 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:12 http://incoming.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
-Get:13 http://incoming.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
-Get:14 http://incoming.debian.org sid/main kfreebsd-amd64 2011-10-29-0215.35.pdiff [17.9 kB]
-Get:15 http://incoming.debian.org sid/contrib kfreebsd-amd64 2011-10-29-0215.35.pdiff [31 B]
-Get:16 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [86.9 kB]
-Get:17 http://incoming.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Get:18 http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:19 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
-Get:20 http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex [2023 B]
-Get:21 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex [2023 B]
+Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Get:22 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
+Hit http://mirror-ubc.debian.org sid/main TranslationIndex
Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Get:23 http://mirror-ubc.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
-Get:24 http://mirror-ubc.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
-Get:25 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-10-29-0215.35.pdiff [17.9 kB]
-Get:26 http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 2011-10-29-0215.35.pdiff [31 B]
-Get:27 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [86.9 kB]
-Get:28 http://incoming.debian.org Sources [36.2 kB]
-Get:29 http://incoming.debian.org Packages [324 kB]
-Get:30 http://incoming.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
-Get:31 http://incoming.debian.org sid/main kfreebsd-amd64 2011-10-29-0215.35.pdiff [17.9 kB]
+Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages
Ign http://mirror-ubc.debian.org sid/contrib Translation-en
Ign http://mirror-ubc.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org Release.gpg
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
+Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Ign http://incoming.debian.org sid/non-free TranslationIndex
+Hit http://incoming.debian.org Release
+Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Ign http://incoming.debian.org sid/contrib Translation-en
-Get:32 http://incoming.debian.org sid/contrib kfreebsd-amd64 2011-10-29-0215.35.pdiff [31 B]
-Get:33 http://mirror-ubc.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Get:34 http://mirror-ubc.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
-Get:35 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-10-29-0215.35.pdiff [17.9 kB]
-Get:36 http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 2011-10-29-0215.35.pdiff [31 B]
-Fetched 914 kB in 15s (57.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -108,11 +91,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 1s (635 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 1s (544 kB/s)
Download complete and in download only mode
Check arch
@@ -132,12 +115,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -152,7 +135,7 @@ bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
+diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.1)
e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1)
@@ -199,12 +182,12 @@ The following NEW packages will be installed:
libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 5 not upgraded.
Need to get 0 B/8237 kB of archives.
-After this operation, 21.7 MB of additional disk space will be used.
+After this operation, 21.6 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 12406 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-amd64.deb) ...
+(Reading database ... 12290 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_kfreebsd-amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-amd64.deb) ...
Selecting previously unselected package libxml2.
@@ -239,7 +222,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-amd64.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpipeline1 (1.2.0-4) ...
Setting up libglib2.0-0 (2.28.8-1) ...
No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
@@ -263,11 +246,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 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 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_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_1:3.0-1 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 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.1-15 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-15 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 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 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 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 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 type-handling_0.2.23 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 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_4.6.1-15 gcc-4.6_4.6.1-15 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15
+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 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_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 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.1-15 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_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_1.2.0-4 libpng12-0_1.2.46-3 libquadmath0_4.6.1-15 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 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 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 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 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 type-handling_0.2.23 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 │
@@ -278,12 +261,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -294,24 +277,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -324,21 +307,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -510,6 +493,13 @@ 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
@@ -585,7 +575,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -630,22 +620,22 @@ 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_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.13.4-1_kfreebsd-amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.14.2-1_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0316
+Build finished at 20111103-0414
-bedtools_2.13.4-1_kfreebsd-amd64.changes:
+bedtools_2.14.2-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-amd64
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
@@ -653,33 +643,33 @@ 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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- a4cd93bbd55049562234e90038e5de946a39575d 668126 bedtools_2.13.4-1_kfreebsd-amd64.deb
+ 2d0a50f22da7fa251de54ce643e56d183124a202 671650 bedtools_2.14.2-1_kfreebsd-amd64.deb
Checksums-Sha256:
- d8603b9d6826c48fa3d4c838d699cef7b90da8d68ebed7f195ed9d357c3845e5 668126 bedtools_2.13.4-1_kfreebsd-amd64.deb
+ e61b976c62901722a398acc0792398dbde0f41f234b1bce5be3ffd1717d8f3e7 671650 bedtools_2.14.2-1_kfreebsd-amd64.deb
Files:
- 21afb051f4c03c7e2b238801fd6b0c8c 668126 science optional bedtools_2.13.4-1_kfreebsd-amd64.deb
+ 50b1b648289932f5cd976ce679dc5a68 671650 science optional bedtools_2.14.2-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_kfreebsd-amd64.deb
+bedtools_2.14.2-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 668126 bytes: control archive= 1741 bytes.
+ size 671650 bytes: control archive= 1741 bytes.
876 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4663
+ Installed-Size: 4665
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -695,49 +685,49 @@ bedtools_2.13.4-1_kfreebsd-amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 03:16 ./
-drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 03:13 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/bin/
--rwxr-xr-x root/root 110000 2011-10-29 03:16 ./usr/bin/annotateBed
--rwxr-xr-x root/root 218376 2011-10-29 03:16 ./usr/bin/bamToBed
--rwxr-xr-x root/root 101856 2011-10-29 03:16 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 229232 2011-10-29 03:16 ./usr/bin/bedToBam
--rwxr-xr-x root/root 126480 2011-10-29 03:16 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 126496 2011-10-29 03:16 ./usr/bin/closestBed
--rwxr-xr-x root/root 114168 2011-10-29 03:16 ./usr/bin/complementBed
--rwxr-xr-x root/root 276440 2011-10-29 03:16 ./usr/bin/coverageBed
--rwxr-xr-x root/root 147112 2011-10-29 03:16 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 118768 2011-10-29 03:16 ./usr/bin/flankBed
--rwxr-xr-x root/root 294888 2011-10-29 03:16 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 345520 2011-10-29 03:16 ./usr/bin/intersectBed
--rwxr-xr-x root/root 110096 2011-10-29 03:16 ./usr/bin/linksBed
--rwxr-xr-x root/root 118328 2011-10-29 03:16 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 114112 2011-10-29 03:16 ./usr/bin/mergeBed
--rwxr-xr-x root/root 292760 2011-10-29 03:16 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 147136 2011-10-29 03:16 ./usr/bin/nucBed
--rwxr-xr-x root/root 93664 2011-10-29 03:16 ./usr/bin/overlap
--rwxr-xr-x root/root 356352 2011-10-29 03:16 ./usr/bin/pairToBed
--rwxr-xr-x root/root 179944 2011-10-29 03:16 ./usr/bin/pairToPair
--rwxr-xr-x root/root 135232 2011-10-29 03:16 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 110056 2011-10-29 03:16 ./usr/bin/slopBed
--rwxr-xr-x root/root 150952 2011-10-29 03:16 ./usr/bin/sortBed
--rwxr-xr-x root/root 267640 2011-10-29 03:16 ./usr/bin/tagBam
--rwxr-xr-x root/root 118192 2011-10-29 03:16 ./usr/bin/subtractBed
--rwxr-xr-x root/root 65032 2011-10-29 03:16 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 278800 2011-10-29 03:16 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-11-03 04:13 ./
+drwxr-xr-x root/root 0 2011-11-03 04:13 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 04:14 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 04:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 04:14 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-03 04:14 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 04:09 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-03 04:14 ./usr/bin/
+-rwxr-xr-x root/root 110000 2011-11-03 04:14 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 218376 2011-11-03 04:14 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 101856 2011-11-03 04:14 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 229232 2011-11-03 04:14 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 126480 2011-11-03 04:14 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 126656 2011-11-03 04:14 ./usr/bin/closestBed
+-rwxr-xr-x root/root 114168 2011-11-03 04:14 ./usr/bin/complementBed
+-rwxr-xr-x root/root 276592 2011-11-03 04:14 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 147112 2011-11-03 04:14 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 118920 2011-11-03 04:14 ./usr/bin/flankBed
+-rwxr-xr-x root/root 294888 2011-11-03 04:14 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 345672 2011-11-03 04:14 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 110248 2011-11-03 04:14 ./usr/bin/linksBed
+-rwxr-xr-x root/root 118328 2011-11-03 04:14 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 114112 2011-11-03 04:14 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 292912 2011-11-03 04:14 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 147136 2011-11-03 04:14 ./usr/bin/nucBed
+-rwxr-xr-x root/root 93664 2011-11-03 04:14 ./usr/bin/overlap
+-rwxr-xr-x root/root 356352 2011-11-03 04:14 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 180096 2011-11-03 04:14 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 135384 2011-11-03 04:14 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 110200 2011-11-03 04:14 ./usr/bin/slopBed
+-rwxr-xr-x root/root 150952 2011-11-03 04:14 ./usr/bin/sortBed
+-rwxr-xr-x root/root 267792 2011-11-03 04:14 ./usr/bin/tagBam
+-rwxr-xr-x root/root 118192 2011-11-03 04:14 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 65032 2011-11-03 04:14 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 278952 2011-11-03 04:14 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -751,11 +741,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1319857958-32760/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1320293343-26755/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -763,9 +753,9 @@ The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 18 to remove and 10 not upgraded.
-After this operation, 21.7 MB disk space will be freed.
-(Reading database ... 13582 files and directories currently installed.)
+0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded.
+After this operation, 21.6 MB disk space will be freed.
+(Reading database ... 13466 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -799,18 +789,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 135716
-Build-Time: 196
+Build-Space: 137236
+Build-Time: 285
Distribution: sid
-Install-Time: 32
-Job: bedtools_2.13.4-1
+Install-Time: 34
+Job: bedtools_2.14.2-1
Package: bedtools
-Package-Time: 257
-Source-Version: 2.13.4-1
-Space: 135716
+Package-Time: 331
+Source-Version: 2.14.2-1
+Space: 137236
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0316
-Build needed 00:04:17, 135716k disc space
-Signature with key '911EAB69' requested:
+Finished at 20111103-0414
+Build needed 00:05:31, 137236k disc space
+Signature with key 'D33FE1D8' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index de8f309..953072a 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,65 +1,59 @@
-From buildd at field.debian.org Sat Oct 29 04:01:35 2011
-Return-path: <buildd at field.debian.org>
+From buildd at finzi.debian.org Thu Nov 03 03:45:55 2011
+Return-path: <buildd at finzi.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at field.debian.org>)
- id 1RK06x-0000Ax-Lv
- for logs at buildd.debian.org; Sat, 29 Oct 2011 04:01:35 +0000
-Received: from field.debian.org ([194.177.211.210])
+ (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
+ id 1RLoFW-0002vE-Si
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 03:45:54 +0000
+Received: from finzi.debian.org ([206.12.19.111])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
+ CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at field.debian.org>)
- id 1RK06w-0001Sw-5c; Sat, 29 Oct 2011 04:01:34 +0000
-Received: from buildd by field.debian.org with local (Exim 4.72)
- (envelope-from <buildd at field.debian.org>)
- id 1RK06v-000OcF-B1; Sat, 29 Oct 2011 04:01:33 +0000
-Message-Id: <E1RK06v-000OcF-B1 at field.debian.org>
+ (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
+ id 1RLoFV-0006XB-O9; Thu, 03 Nov 2011 03:45:54 +0000
+Received: from buildd by finzi.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at finzi.debian.org>)
+ id 1RLoFQ-000GLL-Jh; Thu, 03 Nov 2011 03:45:48 +0000
+Message-Id: <E1RLoFQ-000GLL-Jh at finzi.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 29 Oct 2011 04:01:33 +0000
-From: buildd on field <buildd at field.debian.org>
+Date: Thu, 3 Nov 2011 03:45:48 +0000
+From: buildd on finzi <buildd at finzi.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on kfreebsd-i386
+Subject: Log for successful build of bedtools_2.14.2-1 on kfreebsd-i386
(dist=sid)
-Key-Id: 6B8016EE
+Key-Id: D859A500
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (kfreebsd-i386) 29 Oct 2011 03:55 ║
+║ bedtools 2.14.2-1 (kfreebsd-i386) 03 Nov 2011 03:40 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: kfreebsd-i386
-Get:1 http://ftp.gr.debian.org sid InRelease [146 kB]
-Get:2 http://ftp.gr.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Get:3 http://ftp.gr.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:4 http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
-Get:5 http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex [2023 B]
-Get:6 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex [2023 B]
-Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
-Get:7 http://ftp.gr.debian.org sid/main TranslationIndex [2045 B]
-Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Get:8 http://ftp.gr.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
+Hit http://mirror-ubc.debian.org sid InRelease
+Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:9 http://ftp.gr.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
-Get:10 http://ftp.gr.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
-Get:11 http://ftp.gr.debian.org sid/main kfreebsd-i386 2011-10-29-0215.35.pdiff [17.0 kB]
-Get:12 http://ftp.gr.debian.org sid/contrib kfreebsd-i386 2011-10-29-0215.35.pdiff [31 B]
-Get:13 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2011-10-29-0215.35.pdiff [31 B]
-Ign http://ftp.gr.debian.org sid/contrib Translation-en
-Ign http://ftp.gr.debian.org sid/non-free Translation-en
-Get:14 http://incoming.debian.org Release.gpg [836 B]
+Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
+Hit http://mirror-ubc.debian.org sid/main TranslationIndex
+Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
+Hit http://incoming.debian.org Release.gpg
+Ign http://mirror-ubc.debian.org sid/contrib Translation-en
+Ign http://mirror-ubc.debian.org sid/non-free Translation-en
Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
@@ -69,17 +63,12 @@ Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:15 http://incoming.debian.org Release [1604 B]
-Get:16 http://ftp.gr.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
-Get:17 http://ftp.gr.debian.org sid/main kfreebsd-i386 2011-10-29-0215.35.pdiff [17.0 kB]
-Get:18 http://incoming.debian.org Sources [36.6 kB]
-Get:19 http://incoming.debian.org Packages [331 kB]
-Get:20 http://ftp.gr.debian.org sid/contrib kfreebsd-i386 2011-10-29-0215.35.pdiff [31 B]
-Get:21 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2011-10-29-0215.35.pdiff [31 B]
+Hit http://incoming.debian.org Release
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 558 kB in 6s (90.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -100,11 +89,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 2s (347 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 1s (601 kB/s)
Download complete and in download only mode
Check arch
@@ -124,12 +113,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -144,7 +133,7 @@ bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
+diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.1)
e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1)
@@ -178,26 +167,25 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
- po-debconf
+ diffstat file gettext gettext-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
procmail graphviz
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 10 not upgraded.
-Need to get 0 B/9192 kB of archives.
-After this operation, 24.2 MB of additional disk space will be used.
+0 upgraded, 18 newly installed, 0 to remove and 5 not upgraded.
+Need to get 0 B/8099 kB of archives.
+After this operation, 21.1 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 12054 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-i386.deb) ...
+(Reading database ... 14032 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_kfreebsd-i386.deb) ...
Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-i386.deb) ...
Selecting previously unselected package libxml2.
@@ -206,8 +194,6 @@ Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-i386.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libmagic1.
@@ -234,13 +220,12 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpipeline1 (1.2.0-4) ...
Setting up libglib2.0-0 (2.28.8-1) ...
No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
-Setting up groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
@@ -259,11 +244,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-1 gcc-4.6_4.6.2-1 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 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-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 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 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.2-1 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 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 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-1 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.2-1 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 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 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 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 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 type-handling_0.2.23 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 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 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3
+Package versions: apt_0.8.15.9 autotools-dev_20110511.1 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 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 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 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 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 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.12-1 libgomp1_4.6.2-3 libgpg-error0_1.10-1 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libp11-kit0_0.7-2 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_1.2.0-4 libpng12-0_1.2.46-3 libquadmath0_4.6.2-3 libreadline6_6.2-7 libsasl2-2_2.1.25.dfsg1-2 libsbuf0_8.2+ds1-4 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 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 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 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.47 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 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 tzdata_2011n-1 util-linux_2.19.1-5 vim_2:7.3.346-1 vim-common_2:7.3.346-1 vim-runtime_2:7.3.346-1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -274,12 +259,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -290,24 +275,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -320,21 +305,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -506,6 +491,13 @@ 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
@@ -581,7 +573,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -626,56 +618,56 @@ 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_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bedtools_2.13.4-1_kfreebsd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bedtools_2.14.2-1_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0400
+Build finished at 20111103-0345
-bedtools_2.13.4-1_kfreebsd-i386.changes:
+bedtools_2.14.2-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-i386
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
+Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- 92a56f473957115d23cd8906ee1928760a93e063 679346 bedtools_2.13.4-1_kfreebsd-i386.deb
+ dcab0cf745f3d30ea9a98bf0df91de052f5ea5cf 682388 bedtools_2.14.2-1_kfreebsd-i386.deb
Checksums-Sha256:
- 6927d84913f1bd96a7c3b07aca308a08807125f0f3a4a6f5cbbb1d3fbbe30580 679346 bedtools_2.13.4-1_kfreebsd-i386.deb
+ b4015ec543568cc051d184d2daab623f6b4961a1517cf156a89c1f5ffe5a453b 682388 bedtools_2.14.2-1_kfreebsd-i386.deb
Files:
- 0fe4a69daf0e253938a20f1eb6f67412 679346 science optional bedtools_2.13.4-1_kfreebsd-i386.deb
+ 9c755d1980e2143dfc29a31ae375d702 682388 science optional bedtools_2.14.2-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_kfreebsd-i386.deb
+bedtools_2.14.2-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 679346 bytes: control archive= 1742 bytes.
+ size 682388 bytes: control archive= 1735 bytes.
875 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4602
+ Installed-Size: 4611
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -691,49 +683,49 @@ bedtools_2.13.4-1_kfreebsd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 04:00 ./
-drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 03:57 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/bin/
--rwxr-xr-x root/root 102932 2011-10-29 04:00 ./usr/bin/annotateBed
--rwxr-xr-x root/root 223468 2011-10-29 04:00 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96356 2011-10-29 04:00 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227628 2011-10-29 04:00 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121132 2011-10-29 04:00 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 121600 2011-10-29 04:00 ./usr/bin/closestBed
--rwxr-xr-x root/root 105084 2011-10-29 04:00 ./usr/bin/complementBed
--rwxr-xr-x root/root 281428 2011-10-29 04:00 ./usr/bin/coverageBed
--rwxr-xr-x root/root 142096 2011-10-29 04:00 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 113848 2011-10-29 04:00 ./usr/bin/flankBed
--rwxr-xr-x root/root 298052 2011-10-29 04:00 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 350572 2011-10-29 04:00 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105300 2011-10-29 04:00 ./usr/bin/linksBed
--rwxr-xr-x root/root 109244 2011-10-29 04:00 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 106708 2011-10-29 04:00 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297312 2011-10-29 04:00 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 142012 2011-10-29 04:00 ./usr/bin/nucBed
--rwxr-xr-x root/root 88164 2011-10-29 04:00 ./usr/bin/overlap
--rwxr-xr-x root/root 366968 2011-10-29 04:00 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178284 2011-10-29 04:00 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129160 2011-10-29 04:00 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 104956 2011-10-29 04:00 ./usr/bin/slopBed
--rwxr-xr-x root/root 142620 2011-10-29 04:00 ./usr/bin/sortBed
--rwxr-xr-x root/root 272744 2011-10-29 04:00 ./usr/bin/tagBam
--rwxr-xr-x root/root 112716 2011-10-29 04:00 ./usr/bin/subtractBed
--rwxr-xr-x root/root 59616 2011-10-29 04:00 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285024 2011-10-29 04:00 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 03:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 03:45 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-03 03:45 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 03:42 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-03 03:45 ./usr/bin/
+-rwxr-xr-x root/root 103224 2011-11-03 03:45 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 223468 2011-11-03 03:45 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96356 2011-11-03 03:45 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227672 2011-11-03 03:45 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121488 2011-11-03 03:45 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 121988 2011-11-03 03:45 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105440 2011-11-03 03:45 ./usr/bin/complementBed
+-rwxr-xr-x root/root 281784 2011-11-03 03:45 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 142452 2011-11-03 03:45 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 114172 2011-11-03 03:45 ./usr/bin/flankBed
+-rwxr-xr-x root/root 301420 2011-11-03 03:45 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 350572 2011-11-03 03:45 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105656 2011-11-03 03:45 ./usr/bin/linksBed
+-rwxr-xr-x root/root 109568 2011-11-03 03:45 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 107032 2011-11-03 03:45 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297312 2011-11-03 03:45 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 142392 2011-11-03 03:45 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88164 2011-11-03 03:45 ./usr/bin/overlap
+-rwxr-xr-x root/root 366968 2011-11-03 03:45 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178284 2011-11-03 03:45 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129424 2011-11-03 03:45 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 105312 2011-11-03 03:45 ./usr/bin/slopBed
+-rwxr-xr-x root/root 142976 2011-11-03 03:45 ./usr/bin/sortBed
+-rwxr-xr-x root/root 272744 2011-11-03 03:45 ./usr/bin/tagBam
+-rwxr-xr-x root/root 112716 2011-11-03 03:45 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 59616 2011-11-03 03:45 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285024 2011-11-03 03:45 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -747,21 +739,21 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1319860544-91264/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1320291640-59931/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
- libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 10 not upgraded.
-After this operation, 24.2 MB disk space will be freed.
-(Reading database ... 13410 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
+ libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded.
+After this operation, 21.1 MB disk space will be freed.
+(Reading database ... 15206 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -772,10 +764,6 @@ Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
@@ -784,6 +772,8 @@ Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
+Removing man-db ...
+Purging configuration files for man-db ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
@@ -797,18 +787,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 95096
-Build-Time: 187
+Build-Space: 96054
+Build-Time: 204
Distribution: sid
-Install-Time: 80
-Job: bedtools_2.13.4-1
+Install-Time: 36
+Job: bedtools_2.14.2-1
Package: bedtools
-Package-Time: 294
-Source-Version: 2.13.4-1
-Space: 95096
+Package-Time: 287
+Source-Version: 2.14.2-1
+Space: 96054
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0400
-Build needed 00:04:54, 95096k disc space
-Signature with key '6B8016EE' requested:
+Finished at 20111103-0345
+Build needed 00:04:47, 96054k disc space
+Signature with key 'D859A500' requested:
diff --git a/mips.log b/mips.log
index d14b130..91f837a 100644
--- a/mips.log
+++ b/mips.log
@@ -1,67 +1,68 @@
-From buildd at ball.debian.org Sat Oct 29 03:27:17 2011
-Return-path: <buildd at ball.debian.org>
+From buildd at lucatelli.debian.org Thu Nov 03 04:37:28 2011
+Return-path: <buildd at lucatelli.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
- id 1RJzZl-0003dp-Ml
- for logs at buildd.debian.org; Sat, 29 Oct 2011 03:27:17 +0000
-Received: from ball.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d09])
+ (Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
+ id 1RLp3Q-0002Bi-1L
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:37:28 +0000
+Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=ball.debian.org, EMAIL=hostmaster at ball.debian.org (verified)
+ CN=lucatelli.debian.org,
+ EMAIL=hostmaster at lucatelli.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
- id 1RJzZl-0000Ss-0B
- for logs at buildd.debian.org; Sat, 29 Oct 2011 03:27:17 +0000
-Received: from buildd by ball.debian.org with local (Exim 4.72)
- (envelope-from <buildd at ball.debian.org>)
- id 1RJzZk-0004Ud-A5; Sat, 29 Oct 2011 03:27:16 +0000
-Date: Sat, 29 Oct 2011 03:27:16 +0000
-Message-Id: <E1RJzZk-0004Ud-A5 at ball.debian.org>
-From: buildd on ball <buildd at ball.debian.org>
-To: logs at buildd.debian.org,buildd-porters at ball.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on mips (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
+ id 1RLp3O-0004gH-BS
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:37:26 +0000
+Received: from buildd by lucatelli.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at lucatelli.debian.org>) id 1RLp3I-0006tu-Je
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:37:20 +0000
+From: buildd on lucatelli <buildd at lucatelli.debian.org>
+To: logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.14.2-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1RLp3I-0006tu-Je at lucatelli.debian.org>
+Date: Thu, 03 Nov 2011 04:37:20 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ball.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (mips) 29 Oct 2011 03:04 ║
+║ bedtools 2.14.2-1 (mips) 03 Nov 2011 03:58 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: mips
-Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
+Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [5868 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5889 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5874 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [56.5 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [104 kB]
-Get:8 http://ftp.de.debian.org unstable/main mips Packages [7593 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib mips Packages [55.7 kB]
-Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [56.9 kB]
+Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [104 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7601 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [55.8 kB]
+Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
+Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [7596 kB]
-Get:14 http://incoming.debian.org unstable/contrib mips Packages [55.5 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [7601 kB]
+Get:14 http://incoming.debian.org unstable/contrib mips Packages [55.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [36.2 kB]
-Get:18 http://incoming.debian.org Packages [324 kB]
+Get:17 http://incoming.debian.org Sources [40.9 kB]
+Get:18 http://incoming.debian.org Packages [602 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.0 MB in 51s (544 kB/s)
+Fetched 28.4 MB in 1min 21s (348 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 1s (714 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 1s (798 kB/s)
Download complete and in download only mode
Check arch
@@ -106,12 +107,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 33 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 33 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -173,35 +174,35 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 33 not upgraded.
Need to get 9581 kB of archives.
After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-3 [35.6 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.8-1 [1565 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-5 [858 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-2 [104 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libmagic1 mips 5.09-2 [249 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main file mips 5.09-2 [51.8 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-4 [35.3 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.8-1 [1565 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-5 [858 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-2 [104 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.09-2 [249 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.09-2 [51.8 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9581 kB in 1s (6315 kB/s)
+Fetched 9581 kB in 1s (6016 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10544 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mips.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_mips.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -242,7 +243,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.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.
@@ -271,11 +272,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 33 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-sb1-bcm91250a mips (mips64)
+Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 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_4.6.1-15 dash_0.5.7-2 debconf_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_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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-13.11 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 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_1.3.3-15 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 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_4.6.1-15 dash_0.5.7-2 debconf_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_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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-13.11 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 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_1.3.3-15 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -286,12 +287,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -307,24 +308,24 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIF
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -337,21 +338,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -527,6 +528,13 @@ 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
@@ -602,7 +610,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -647,56 +655,56 @@ 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_mips.deb'.
- dpkg-genchanges -B -mDebian Build Daemon <buildd_mips-ball at buildd.debian.org> >../bedtools_2.13.4-1_mips.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../bedtools_2.14.2-1_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0327
+Build finished at 20111103-0437
-bedtools_2.13.4-1_mips.changes:
+bedtools_2.14.2-1_mips.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: mips
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
-Maintainer: Debian Build Daemon <buildd_mips-ball at buildd.debian.org>
+Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- e545407436619ad8024731ff1087ca1352c82ab5 596388 bedtools_2.13.4-1_mips.deb
+ 96b3b284a9a56b05f39c176832ded7ba2c5650c4 599578 bedtools_2.14.2-1_mips.deb
Checksums-Sha256:
- 5012df456da793ae416d33afd9d28b8a4929cc09ca542280f263b45f0dbfe099 596388 bedtools_2.13.4-1_mips.deb
+ 6cbd44fd6097408f6f9d7a4a22d1205f12d6eb7c526966f2564e0e6c19ce16cc 599578 bedtools_2.14.2-1_mips.deb
Files:
- 8e2542ad9b10589c3f205b77ed0dde1f 596388 science optional bedtools_2.13.4-1_mips.deb
+ 25a633d0694718d857c6278c510beb7d 599578 science optional bedtools_2.14.2-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_mips.deb
+bedtools_2.14.2-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 596388 bytes: control archive= 1732 bytes.
+ size 599578 bytes: control archive= 1737 bytes.
866 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5008
+ Installed-Size: 5015
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -712,49 +720,7 @@ bedtools_2.13.4-1_mips.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 03:25 ./
-drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 03:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/bin/
--rwxr-xr-x root/root 112024 2011-10-29 03:26 ./usr/bin/annotateBed
--rwxr-xr-x root/root 103848 2011-10-29 03:26 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 114184 2011-10-29 03:26 ./usr/bin/linksBed
--rwxr-xr-x root/root 128600 2011-10-29 03:26 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 299084 2011-10-29 03:26 ./usr/bin/tagBam
--rwxr-xr-x root/root 139592 2011-10-29 03:26 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 307068 2011-10-29 03:26 ./usr/bin/coverageBed
--rwxr-xr-x root/root 118552 2011-10-29 03:26 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 116536 2011-10-29 03:26 ./usr/bin/mergeBed
--rwxr-xr-x root/root 152828 2011-10-29 03:26 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 152552 2011-10-29 03:26 ./usr/bin/sortBed
--rwxr-xr-x root/root 63960 2011-10-29 03:26 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 326540 2011-10-29 03:26 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 324412 2011-10-29 03:26 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 248076 2011-10-29 03:26 ./usr/bin/bedToBam
--rwxr-xr-x root/root 187048 2011-10-29 03:26 ./usr/bin/pairToPair
--rwxr-xr-x root/root 152956 2011-10-29 03:26 ./usr/bin/nucBed
--rwxr-xr-x root/root 129224 2011-10-29 03:26 ./usr/bin/closestBed
--rwxr-xr-x root/root 311532 2011-10-29 03:26 ./usr/bin/windowBed
--rwxr-xr-x root/root 93976 2011-10-29 03:26 ./usr/bin/overlap
--rwxr-xr-x root/root 121576 2011-10-29 03:26 ./usr/bin/flankBed
--rwxr-xr-x root/root 244460 2011-10-29 03:26 ./usr/bin/bamToBed
--rwxr-xr-x root/root 120440 2011-10-29 03:26 ./usr/bin/subtractBed
--rwxr-xr-x root/root 378380 2011-10-29 03:26 ./usr/bin/intersectBed
--rwxr-xr-x root/root 114664 2011-10-29 03:26 ./usr/bin/slopBed
--rwxr-xr-x root/root 391308 2011-10-29 03:26 ./usr/bin/pairToBed
--rwxr-xr-x root/root 114776 2011-10-29 03:26 ./usr/bin/complementBed
+dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-a2376810-8eb9-448a-b380-f078d7a1d694/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools_2.14.2-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -768,7 +734,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-8d522319-ac2d-4b70-b8ed-91a448eb589f/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd
+Purging /var/lib/schroot/mount/sid-mips-sbuild-a2376810-8eb9-448a-b380-f078d7a1d694/build/buildd-bedtools_2.14.2-1-mips-oSMen2
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -776,78 +742,86 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 102348
-Build-Time: 1145
+Build-Space: 103176
+Build-Time: 2104
Distribution: sid
-Install-Time: 91
-Job: bedtools_2.13.4-1
+Install-Time: 74
+Job: bedtools_2.14.2-1
Package: bedtools
-Package-Time: 1374
-Source-Version: 2.13.4-1
-Space: 102348
+Package-Time: 2306
+Source-Version: 2.14.2-1
+Space: 103176
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0327
-Build needed 00:22:54, 102348k disc space
-Signature with key '2D578AB1' requested:
-
-From buildd at phrixos.ayous.org Sat Oct 29 04:32:47 2011
-Return-path: <buildd at phrixos.ayous.org>
-Received: from phrixos.ayous.org ([2001:a60:f006:deb:223:9eff:fe00:f7c]
- helo=alius.ayous.org)
+Finished at 20111103-0437
+Build needed 00:38:26, 103176k disc space
+Signature with key 'FDFDA76A' requested:
+
+From buildd at eysler.debian.org Thu Nov 03 04:40:33 2011
+Return-path: <buildd at eysler.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at phrixos.ayous.org>)
- id 1RK0b7-0004Vw-IW
- for logs at buildd.debian.org; Sat, 29 Oct 2011 04:32:47 +0000
-Received: from buildd by phrixos.ayous.org with local (Exim 4.72)
- (envelope-from <buildd at phrixos.ayous.org>)
- id 1RK0b5-0006uY-3C; Sat, 29 Oct 2011 04:32:43 +0000
-Date: Sat, 29 Oct 2011 04:32:43 +0000
-Message-Id: <E1RK0b5-0006uY-3C at phrixos.ayous.org>
-From: buildd on phrixos <buildd at phrixos.ayous.org>
-To: aba+buildd_phrixos at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on mipsel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at eysler.debian.org>)
+ id 1RLp6P-0002jm-HV
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:33 +0000
+Received: from eysler.debian.org ([2001:858:2:2:1a1a:0:563b:7698])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=eysler.debian.org, EMAIL=hostmaster at eysler.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at eysler.debian.org>)
+ id 1RLp6O-0004sl-PU
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:32 +0000
+Received: from buildd by eysler.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at eysler.debian.org>) id 1RLp6U-00021C-4K
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:38 +0000
+Date: Thu, 03 Nov 2011 04:40:38 +0000
+Message-Id: <E1RLp6U-00021C-4K at eysler.debian.org>
+From: buildd on eysler <buildd at eysler.debian.org>
+To: logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.14.2-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on phrixos.ayous.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on eysler.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (mipsel) 29 Oct 2011 04:10 ║
+║ bedtools 2.14.2-1 (mipsel) 03 Nov 2011 04:12 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-30419245-bcd1-4c75-8da2-a8d7e08091c4/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk
-Start Time: 20111029-0410
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://mirror.ayous.org unstable InRelease [146 kB]
-Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:3 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
-Get:4 http://mirror.ayous.org unstable/main Sources [7388 kB]
+Get:1 http://ftp.at.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
Ign http://incoming.debian.org InRelease
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1604 B]
+Get:5 http://ftp.at.debian.org unstable/main Sources [5889 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:7 http://ftp.at.debian.org unstable/contrib Sources [56.9 kB]
+Get:8 http://ftp.at.debian.org unstable/non-free Sources [104 kB]
+Get:9 http://ftp.at.debian.org unstable/main mipsel Packages [7604 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:12 http://incoming.debian.org unstable/main mipsel Packages [7603 kB]
+Get:13 http://ftp.at.debian.org unstable/contrib mipsel Packages [56.1 kB]
+Ign http://ftp.at.debian.org unstable/contrib TranslationIndex
+Get:14 http://ftp.at.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.at.debian.org unstable/contrib Translation-en
+Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [56.1 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:5 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:6 http://mirror.ayous.org unstable/contrib Sources [67.7 kB]
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://mirror.ayous.org unstable/non-free Sources [125 kB]
-Get:9 http://incoming.debian.org unstable/main Sources [7388 kB]
-Get:10 http://mirror.ayous.org unstable/main mipsel Packages [9956 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [67.7 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [125 kB]
-Get:13 http://incoming.debian.org unstable/main mipsel Packages [9956 kB]
-Get:14 http://mirror.ayous.org unstable/contrib mipsel Packages [68.0 kB]
-Ign http://mirror.ayous.org unstable/contrib Translation-en
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [68.0 kB]
-Get:16 http://incoming.debian.org Release [1604 B]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Get:17 http://incoming.debian.org Sources [43.1 kB]
-Get:18 http://incoming.debian.org Packages [515 kB]
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [40.9 kB]
+Get:18 http://incoming.debian.org Packages [606 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 36.1 MB in 31s (1140 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 28.4 MB in 1min 38s (287 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -868,30 +842,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 3s (272 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 1s (619 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.18.1-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install bedtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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
+Checking for already installed dependencies...
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
+bash: already installed (4.1-3)
+coreutils: already installed (8.13-3)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.4)
+diffutils: already installed (1:3.0-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+findutils: already installed (4.4.2-1+b1)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
+hostname: already installed (3.06)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-6)
+sed: already installed (4.2.1-9)
+login: already installed (1:4.1.4.2+svn3283-3)
+sysvinit-utils: already installed (2.88dsf-13.12)
+sysvinit: already installed (2.88dsf-13.12)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-21)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -910,35 +933,35 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 20 not upgraded.
-Need to get 9532 kB of archives.
+0 upgraded, 21 newly installed, 0 to remove and 28 not upgraded.
+Need to get 9531 kB of archives.
After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
-Get:20 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+Get:1 http://ftp.at.debian.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-4 [35.2 kB]
+Get:2 http://ftp.at.debian.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
+Get:3 http://ftp.at.debian.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
+Get:4 http://ftp.at.debian.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
+Get:5 http://ftp.at.debian.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
+Get:6 http://ftp.at.debian.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
+Get:7 http://ftp.at.debian.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:8 http://ftp.at.debian.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:9 http://ftp.at.debian.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
+Get:10 http://ftp.at.debian.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
+Get:11 http://ftp.at.debian.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
+Get:12 http://ftp.at.debian.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
+Get:13 http://ftp.at.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://ftp.at.debian.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:15 http://ftp.at.debian.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
+Get:16 http://ftp.at.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://ftp.at.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://ftp.at.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://ftp.at.debian.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
+Get:20 http://ftp.at.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://ftp.at.debian.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9532 kB in 1s (6774 kB/s)
+Fetched 9531 kB in 2s (3410 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10569 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
+(Reading database ... 10699 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_mipsel.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -979,7 +1002,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.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.
@@ -1005,10 +1028,14 @@ Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.36-rc6-loongson-2f mipsel (mips64)
-Toolchain package versions: libc6-dev_2.13-21 dpkg-dev_1.16.1.1 linux-libc-dev_3.0.0-5 gcc-4.6_4.6.1-15 g++-4.6_4.6.1-15 binutils_2.21.90.20111004-2 libstdc++6-4.6-dev_4.6.1-15 libstdc++6_4.6.1-15
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 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_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.39-3-loongson-2e mipsel (mips64)
+Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_2.21.90.20111004-2 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_4.6.1-15 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_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_1.3.3-15 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1018,14 +1045,13 @@ 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: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1036,24 +1062,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture mipsel
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1066,21 +1092,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -1252,6 +1278,13 @@ 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
@@ -1327,10 +1360,10 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -1372,56 +1405,56 @@ 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_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org> >../bedtools_2.13.4-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (eysler) <buildd_mipsel-eysler at buildd.debian.org> >../bedtools_2.14.2-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0432
+Build finished at 20111103-0440
-bedtools_2.13.4-1_mipsel.changes:
+bedtools_2.14.2-1_mipsel.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org>
+Maintainer: mipsel Build Daemon (eysler) <buildd_mipsel-eysler at buildd.debian.org>
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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- fccac36642ee6d1d37fae42e017baea1bafbaf28 629804 bedtools_2.13.4-1_mipsel.deb
+ e85647c71f0767f18a9dabe6367632fbb2ed4dac 630926 bedtools_2.14.2-1_mipsel.deb
Checksums-Sha256:
- d9186686420740adbd60f662f729c891bb225bc438982cd59044dc33143c130c 629804 bedtools_2.13.4-1_mipsel.deb
+ 4dbbefe4686dece182ceaabc365c0e4c38def9d640a83ebfe5136349cc499f66 630926 bedtools_2.14.2-1_mipsel.deb
Files:
- 171d817f4b1fe188910778259ae8b95c 629804 science optional bedtools_2.13.4-1_mipsel.deb
+ b5bf75997bd986267769ec4dcba8ca55 630926 science optional bedtools_2.14.2-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_mipsel.deb
+bedtools_2.14.2-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 629804 bytes: control archive= 1736 bytes.
+ size 630926 bytes: control archive= 1737 bytes.
866 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5005
+ Installed-Size: 5010
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -1437,49 +1470,49 @@ bedtools_2.13.4-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 04:12 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/bin/
--rwxr-xr-x root/root 116424 2011-10-29 04:31 ./usr/bin/mergeBed
--rwxr-xr-x root/root 299084 2011-10-29 04:31 ./usr/bin/tagBam
--rwxr-xr-x root/root 378380 2011-10-29 04:31 ./usr/bin/intersectBed
--rwxr-xr-x root/root 93944 2011-10-29 04:31 ./usr/bin/overlap
--rwxr-xr-x root/root 128600 2011-10-29 04:31 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120104 2011-10-29 04:31 ./usr/bin/subtractBed
--rwxr-xr-x root/root 114776 2011-10-29 04:31 ./usr/bin/complementBed
--rwxr-xr-x root/root 248076 2011-10-29 04:31 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121272 2011-10-29 04:31 ./usr/bin/flankBed
--rwxr-xr-x root/root 118552 2011-10-29 04:31 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 139592 2011-10-29 04:31 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 128696 2011-10-29 04:31 ./usr/bin/closestBed
--rwxr-xr-x root/root 390940 2011-10-29 04:31 ./usr/bin/pairToBed
--rwxr-xr-x root/root 103784 2011-10-29 04:31 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 311532 2011-10-29 04:31 ./usr/bin/windowBed
--rwxr-xr-x root/root 186888 2011-10-29 04:31 ./usr/bin/pairToPair
--rwxr-xr-x root/root 326540 2011-10-29 04:31 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 111928 2011-10-29 04:31 ./usr/bin/annotateBed
--rwxr-xr-x root/root 63960 2011-10-29 04:31 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 152876 2011-10-29 04:31 ./usr/bin/nucBed
--rwxr-xr-x root/root 114664 2011-10-29 04:31 ./usr/bin/slopBed
--rwxr-xr-x root/root 306972 2011-10-29 04:31 ./usr/bin/coverageBed
--rwxr-xr-x root/root 152828 2011-10-29 04:31 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 152104 2011-10-29 04:31 ./usr/bin/sortBed
--rwxr-xr-x root/root 114184 2011-10-29 04:31 ./usr/bin/linksBed
--rwxr-xr-x root/root 324412 2011-10-29 04:31 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 244460 2011-10-29 04:31 ./usr/bin/bamToBed
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 04:18 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/bin/
+-rwxr-xr-x root/root 114248 2011-11-03 04:39 ./usr/bin/linksBed
+-rwxr-xr-x root/root 244460 2011-11-03 04:39 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 307036 2011-11-03 04:39 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 128968 2011-11-03 04:39 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 187256 2011-11-03 04:39 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 114840 2011-11-03 04:39 ./usr/bin/complementBed
+-rwxr-xr-x root/root 116792 2011-11-03 04:39 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 120472 2011-11-03 04:39 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 118616 2011-11-03 04:39 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 104152 2011-11-03 04:39 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 324476 2011-11-03 04:39 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 139656 2011-11-03 04:39 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 114728 2011-11-03 04:39 ./usr/bin/slopBed
+-rwxr-xr-x root/root 311596 2011-11-03 04:39 ./usr/bin/windowBed
+-rwxr-xr-x root/root 94312 2011-11-03 04:39 ./usr/bin/overlap
+-rwxr-xr-x root/root 378444 2011-11-03 04:39 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 112280 2011-11-03 04:39 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 153148 2011-11-03 04:39 ./usr/bin/nucBed
+-rwxr-xr-x root/root 299148 2011-11-03 04:39 ./usr/bin/tagBam
+-rwxr-xr-x root/root 391004 2011-11-03 04:39 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 121624 2011-11-03 04:39 ./usr/bin/flankBed
+-rwxr-xr-x root/root 152972 2011-11-03 04:39 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 248140 2011-11-03 04:39 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 129208 2011-11-03 04:39 ./usr/bin/closestBed
+-rwxr-xr-x root/root 63960 2011-11-03 04:39 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 152472 2011-11-03 04:39 ./usr/bin/sortBed
+-rwxr-xr-x root/root 326604 2011-11-03 04:39 ./usr/bin/multiBamCov
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1488,9 +1521,32 @@ drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-30419245-bcd1-4c75-8da2-a8d7e08091c4/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk
-Not removing build depends: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-bbfa43d9-fdb6-4d10-9e30-1716fbb43730/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mipsel
+Build-Space: 102756
+Build-Time: 1343
+Distribution: sid
+Install-Time: 126
+Job: bedtools_2.14.2-1
+Package: bedtools
+Package-Time: 1655
+Source-Version: 2.14.2-1
+Space: 102756
+Status: successful
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0432
-Build needed 00:22:23, 101932k disc space
+Finished at 20111103-0440
+Build needed 00:27:35, 102756k disc space
+Signature with key '0D12A734' requested:
diff --git a/mipsel.log b/mipsel.log
index 52648a6..c5b26bb 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,59 +1,67 @@
-From buildd at phrixos.ayous.org Sat Oct 29 04:32:47 2011
-Return-path: <buildd at phrixos.ayous.org>
-Received: from phrixos.ayous.org ([2001:a60:f006:deb:223:9eff:fe00:f7c]
- helo=alius.ayous.org)
+From buildd at eysler.debian.org Thu Nov 03 04:40:33 2011
+Return-path: <buildd at eysler.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at phrixos.ayous.org>)
- id 1RK0b7-0004Vw-IW
- for logs at buildd.debian.org; Sat, 29 Oct 2011 04:32:47 +0000
-Received: from buildd by phrixos.ayous.org with local (Exim 4.72)
- (envelope-from <buildd at phrixos.ayous.org>)
- id 1RK0b5-0006uY-3C; Sat, 29 Oct 2011 04:32:43 +0000
-Date: Sat, 29 Oct 2011 04:32:43 +0000
-Message-Id: <E1RK0b5-0006uY-3C at phrixos.ayous.org>
-From: buildd on phrixos <buildd at phrixos.ayous.org>
-To: aba+buildd_phrixos at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on mipsel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at eysler.debian.org>)
+ id 1RLp6P-0002jm-HV
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:33 +0000
+Received: from eysler.debian.org ([2001:858:2:2:1a1a:0:563b:7698])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=eysler.debian.org, EMAIL=hostmaster at eysler.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at eysler.debian.org>)
+ id 1RLp6O-0004sl-PU
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:32 +0000
+Received: from buildd by eysler.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at eysler.debian.org>) id 1RLp6U-00021C-4K
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:38 +0000
+Date: Thu, 03 Nov 2011 04:40:38 +0000
+Message-Id: <E1RLp6U-00021C-4K at eysler.debian.org>
+From: buildd on eysler <buildd at eysler.debian.org>
+To: logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.14.2-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on phrixos.ayous.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on eysler.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (mipsel) 29 Oct 2011 04:10 ║
+║ bedtools 2.14.2-1 (mipsel) 03 Nov 2011 04:12 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-30419245-bcd1-4c75-8da2-a8d7e08091c4/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk
-Start Time: 20111029-0410
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://mirror.ayous.org unstable InRelease [146 kB]
-Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:3 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
-Get:4 http://mirror.ayous.org unstable/main Sources [7388 kB]
+Get:1 http://ftp.at.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
Ign http://incoming.debian.org InRelease
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1604 B]
+Get:5 http://ftp.at.debian.org unstable/main Sources [5889 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:7 http://ftp.at.debian.org unstable/contrib Sources [56.9 kB]
+Get:8 http://ftp.at.debian.org unstable/non-free Sources [104 kB]
+Get:9 http://ftp.at.debian.org unstable/main mipsel Packages [7604 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:12 http://incoming.debian.org unstable/main mipsel Packages [7603 kB]
+Get:13 http://ftp.at.debian.org unstable/contrib mipsel Packages [56.1 kB]
+Ign http://ftp.at.debian.org unstable/contrib TranslationIndex
+Get:14 http://ftp.at.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.at.debian.org unstable/contrib Translation-en
+Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [56.1 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:5 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:6 http://mirror.ayous.org unstable/contrib Sources [67.7 kB]
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://mirror.ayous.org unstable/non-free Sources [125 kB]
-Get:9 http://incoming.debian.org unstable/main Sources [7388 kB]
-Get:10 http://mirror.ayous.org unstable/main mipsel Packages [9956 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [67.7 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [125 kB]
-Get:13 http://incoming.debian.org unstable/main mipsel Packages [9956 kB]
-Get:14 http://mirror.ayous.org unstable/contrib mipsel Packages [68.0 kB]
-Ign http://mirror.ayous.org unstable/contrib Translation-en
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [68.0 kB]
-Get:16 http://incoming.debian.org Release [1604 B]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Get:17 http://incoming.debian.org Sources [43.1 kB]
-Get:18 http://incoming.debian.org Packages [515 kB]
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [40.9 kB]
+Get:18 http://incoming.debian.org Packages [606 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 36.1 MB in 31s (1140 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 28.4 MB in 1min 38s (287 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,30 +82,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 3s (272 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 1s (619 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.18.1-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+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
+Checking for already installed dependencies...
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
+bash: already installed (4.1-3)
+coreutils: already installed (8.13-3)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.4)
+diffutils: already installed (1:3.0-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+findutils: already installed (4.4.2-1+b1)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
+hostname: already installed (3.06)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-6)
+sed: already installed (4.2.1-9)
+login: already installed (1:4.1.4.2+svn3283-3)
+sysvinit-utils: already installed (2.88dsf-13.12)
+sysvinit: already installed (2.88dsf-13.12)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-21)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -116,35 +173,35 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 20 not upgraded.
-Need to get 9532 kB of archives.
+0 upgraded, 21 newly installed, 0 to remove and 28 not upgraded.
+Need to get 9531 kB of archives.
After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
-Get:20 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+Get:1 http://ftp.at.debian.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-4 [35.2 kB]
+Get:2 http://ftp.at.debian.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
+Get:3 http://ftp.at.debian.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
+Get:4 http://ftp.at.debian.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
+Get:5 http://ftp.at.debian.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
+Get:6 http://ftp.at.debian.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
+Get:7 http://ftp.at.debian.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:8 http://ftp.at.debian.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:9 http://ftp.at.debian.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
+Get:10 http://ftp.at.debian.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
+Get:11 http://ftp.at.debian.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
+Get:12 http://ftp.at.debian.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
+Get:13 http://ftp.at.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://ftp.at.debian.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:15 http://ftp.at.debian.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
+Get:16 http://ftp.at.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://ftp.at.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://ftp.at.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://ftp.at.debian.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
+Get:20 http://ftp.at.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://ftp.at.debian.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9532 kB in 1s (6774 kB/s)
+Fetched 9531 kB in 2s (3410 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10569 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
+(Reading database ... 10699 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_mipsel.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -185,7 +242,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.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.
@@ -211,10 +268,14 @@ Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.36-rc6-loongson-2f mipsel (mips64)
-Toolchain package versions: libc6-dev_2.13-21 dpkg-dev_1.16.1.1 linux-libc-dev_3.0.0-5 gcc-4.6_4.6.1-15 g++-4.6_4.6.1-15 binutils_2.21.90.20111004-2 libstdc++6-4.6-dev_4.6.1-15 libstdc++6_4.6.1-15
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 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_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.39-3-loongson-2e mipsel (mips64)
+Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_2.21.90.20111004-2 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_4.6.1-15 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_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_1.3.3-15 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -224,14 +285,13 @@ 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: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -242,24 +302,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture mipsel
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -272,21 +332,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -458,6 +518,13 @@ 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
@@ -533,10 +600,10 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -578,56 +645,56 @@ 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_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org> >../bedtools_2.13.4-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (eysler) <buildd_mipsel-eysler at buildd.debian.org> >../bedtools_2.14.2-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0432
+Build finished at 20111103-0440
-bedtools_2.13.4-1_mipsel.changes:
+bedtools_2.14.2-1_mipsel.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org>
+Maintainer: mipsel Build Daemon (eysler) <buildd_mipsel-eysler at buildd.debian.org>
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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- fccac36642ee6d1d37fae42e017baea1bafbaf28 629804 bedtools_2.13.4-1_mipsel.deb
+ e85647c71f0767f18a9dabe6367632fbb2ed4dac 630926 bedtools_2.14.2-1_mipsel.deb
Checksums-Sha256:
- d9186686420740adbd60f662f729c891bb225bc438982cd59044dc33143c130c 629804 bedtools_2.13.4-1_mipsel.deb
+ 4dbbefe4686dece182ceaabc365c0e4c38def9d640a83ebfe5136349cc499f66 630926 bedtools_2.14.2-1_mipsel.deb
Files:
- 171d817f4b1fe188910778259ae8b95c 629804 science optional bedtools_2.13.4-1_mipsel.deb
+ b5bf75997bd986267769ec4dcba8ca55 630926 science optional bedtools_2.14.2-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_mipsel.deb
+bedtools_2.14.2-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 629804 bytes: control archive= 1736 bytes.
+ size 630926 bytes: control archive= 1737 bytes.
866 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5005
+ Installed-Size: 5010
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -643,49 +710,49 @@ bedtools_2.13.4-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 04:12 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/bin/
--rwxr-xr-x root/root 116424 2011-10-29 04:31 ./usr/bin/mergeBed
--rwxr-xr-x root/root 299084 2011-10-29 04:31 ./usr/bin/tagBam
--rwxr-xr-x root/root 378380 2011-10-29 04:31 ./usr/bin/intersectBed
--rwxr-xr-x root/root 93944 2011-10-29 04:31 ./usr/bin/overlap
--rwxr-xr-x root/root 128600 2011-10-29 04:31 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120104 2011-10-29 04:31 ./usr/bin/subtractBed
--rwxr-xr-x root/root 114776 2011-10-29 04:31 ./usr/bin/complementBed
--rwxr-xr-x root/root 248076 2011-10-29 04:31 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121272 2011-10-29 04:31 ./usr/bin/flankBed
--rwxr-xr-x root/root 118552 2011-10-29 04:31 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 139592 2011-10-29 04:31 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 128696 2011-10-29 04:31 ./usr/bin/closestBed
--rwxr-xr-x root/root 390940 2011-10-29 04:31 ./usr/bin/pairToBed
--rwxr-xr-x root/root 103784 2011-10-29 04:31 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 311532 2011-10-29 04:31 ./usr/bin/windowBed
--rwxr-xr-x root/root 186888 2011-10-29 04:31 ./usr/bin/pairToPair
--rwxr-xr-x root/root 326540 2011-10-29 04:31 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 111928 2011-10-29 04:31 ./usr/bin/annotateBed
--rwxr-xr-x root/root 63960 2011-10-29 04:31 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 152876 2011-10-29 04:31 ./usr/bin/nucBed
--rwxr-xr-x root/root 114664 2011-10-29 04:31 ./usr/bin/slopBed
--rwxr-xr-x root/root 306972 2011-10-29 04:31 ./usr/bin/coverageBed
--rwxr-xr-x root/root 152828 2011-10-29 04:31 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 152104 2011-10-29 04:31 ./usr/bin/sortBed
--rwxr-xr-x root/root 114184 2011-10-29 04:31 ./usr/bin/linksBed
--rwxr-xr-x root/root 324412 2011-10-29 04:31 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 244460 2011-10-29 04:31 ./usr/bin/bamToBed
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 04:18 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/bin/
+-rwxr-xr-x root/root 114248 2011-11-03 04:39 ./usr/bin/linksBed
+-rwxr-xr-x root/root 244460 2011-11-03 04:39 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 307036 2011-11-03 04:39 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 128968 2011-11-03 04:39 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 187256 2011-11-03 04:39 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 114840 2011-11-03 04:39 ./usr/bin/complementBed
+-rwxr-xr-x root/root 116792 2011-11-03 04:39 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 120472 2011-11-03 04:39 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 118616 2011-11-03 04:39 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 104152 2011-11-03 04:39 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 324476 2011-11-03 04:39 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 139656 2011-11-03 04:39 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 114728 2011-11-03 04:39 ./usr/bin/slopBed
+-rwxr-xr-x root/root 311596 2011-11-03 04:39 ./usr/bin/windowBed
+-rwxr-xr-x root/root 94312 2011-11-03 04:39 ./usr/bin/overlap
+-rwxr-xr-x root/root 378444 2011-11-03 04:39 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 112280 2011-11-03 04:39 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 153148 2011-11-03 04:39 ./usr/bin/nucBed
+-rwxr-xr-x root/root 299148 2011-11-03 04:39 ./usr/bin/tagBam
+-rwxr-xr-x root/root 391004 2011-11-03 04:39 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 121624 2011-11-03 04:39 ./usr/bin/flankBed
+-rwxr-xr-x root/root 152972 2011-11-03 04:39 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 248140 2011-11-03 04:39 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 129208 2011-11-03 04:39 ./usr/bin/closestBed
+-rwxr-xr-x root/root 63960 2011-11-03 04:39 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 152472 2011-11-03 04:39 ./usr/bin/sortBed
+-rwxr-xr-x root/root 326604 2011-11-03 04:39 ./usr/bin/multiBamCov
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -694,9 +761,32 @@ drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-30419245-bcd1-4c75-8da2-a8d7e08091c4/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk
-Not removing build depends: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-bbfa43d9-fdb6-4d10-9e30-1716fbb43730/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mipsel
+Build-Space: 102756
+Build-Time: 1343
+Distribution: sid
+Install-Time: 126
+Job: bedtools_2.14.2-1
+Package: bedtools
+Package-Time: 1655
+Source-Version: 2.14.2-1
+Space: 102756
+Status: successful
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0432
-Build needed 00:22:23, 101932k disc space
+Finished at 20111103-0440
+Build needed 00:27:35, 102756k disc space
+Signature with key '0D12A734' requested:
diff --git a/powerpc.log b/powerpc.log
index 15abb42..6d5f2a8 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,68 +1,69 @@
-From buildd at praetorius.debian.org Sat Oct 29 03:09:55 2011
-Return-path: <buildd at praetorius.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at porpora.debian.org Thu Nov 03 03:53:09 2011
+Return-path: <buildd at porpora.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
- id 1RJzIx-0001GN-D5
- for logs at buildd.debian.org; Sat, 29 Oct 2011 03:09:55 +0000
-Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
- (helo=praetorius.debian.org)
+ (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
+ id 1RLoMX-0003oo-N8
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 03:53:09 +0000
+Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
+ helo=porpora.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=praetorius.debian.org,
- EMAIL=hostmaster at praetorius.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
- id 1RJzIw-0007kP-Hw; Sat, 29 Oct 2011 03:09:54 +0000
-Received: from buildd by praetorius.debian.org with local (Exim 4.72)
- (envelope-from <buildd at praetorius.debian.org>)
- id 1RJzIv-0006eJ-Qt; Sat, 29 Oct 2011 03:09:53 +0000
-Date: Sat, 29 Oct 2011 03:09:53 +0000
-Message-Id: <E1RJzIv-0006eJ-Qt at praetorius.debian.org>
-From: buildd on praetorius <buildd at praetorius.debian.org>
-To: wouter at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on powerpc (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
+ CN=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
+ id 1RLoMW-0002sH-Q4; Thu, 03 Nov 2011 03:53:08 +0000
+Received: from buildd by porpora.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at porpora.debian.org>)
+ id 1RLoMW-0003Aq-5F; Thu, 03 Nov 2011 03:53:08 +0000
+Message-Id: <E1RLoMW-0003Aq-5F at porpora.debian.org>
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Thu, 3 Nov 2011 03:53:08 +0000
+From: buildd on porpora <buildd at porpora.debian.org>
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.14.2-1 on powerpc (dist=sid)
+Key-Id: 6CB21D9F
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (powerpc) 29 Oct 2011 03:03 ║
+║ bedtools 2.14.2-1 (powerpc) 03 Nov 2011 03:46 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: powerpc
-Get:1 http://ftp.se.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.se.debian.org unstable/main Sources [5868 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
+Get:2 http://ftp.uk.debian.org unstable/main Sources [5889 kB]
Get:3 http://incoming.debian.org unstable InRelease [146 kB]
-Get:4 http://ftp.se.debian.org unstable/contrib Sources [56.5 kB]
-Get:5 http://ftp.se.debian.org unstable/non-free Sources [104 kB]
-Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [7698 kB]
-Get:7 http://ftp.se.debian.org unstable/contrib powerpc Packages [55.4 kB]
-Ign http://ftp.se.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.se.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.se.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org InRelease
-Get:9 http://incoming.debian.org Release.gpg [836 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5874 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://ftp.uk.debian.org unstable/contrib Sources [56.9 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [104 kB]
+Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7702 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.5 kB]
+Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [7699 kB]
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.2 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [7702 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.5 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [36.2 kB]
-Get:18 http://incoming.debian.org Packages [324 kB]
+Get:17 http://incoming.debian.org Sources [47.2 kB]
+Get:18 http://incoming.debian.org Packages [605 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.2 MB in 17s (1652 kB/s)
+Fetched 28.6 MB in 28s (1014 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 1s (536 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 2s (454 kB/s)
Download complete and in download only mode
Check arch
@@ -101,18 +102,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+fakeroot: already installed (1.18.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 42 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 42 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -124,23 +125,23 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
+coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-09-25-1)
+debianutils: already installed (4.0.4)
+diffutils: already installed (1:3.2-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-2)
ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-5)
+perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
+sysvinit-utils: already installed (2.88dsf-13.12)
+sysvinit: already installed (2.88dsf-13.12)
tar: already installed (1.26-2)
bsdutils: already installed (1:2.19.1-5)
mount: already installed (2.19.1-5)
@@ -149,7 +150,7 @@ libc6-dev: already installed (2.13-21)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
Using default version 8.9.8
@@ -174,35 +175,35 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 42 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 4 not upgraded.
Need to get 9676 kB of archives.
After this operation, 27.8 MB of additional disk space will be used.
-Get:1 http://ftp.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-3 [37.2 kB]
-Get:2 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
-Get:3 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.8-1 [1609 kB]
-Get:4 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5 [837 kB]
-Get:5 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
-Get:6 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:7 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
-Get:8 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:9 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
-Get:10 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
-Get:11 http://ftp.se.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
-Get:12 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
-Get:13 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:15 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
-Get:16 http://ftp.se.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.se.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.se.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://ftp.se.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
-Get:20 http://ftp.se.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.se.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-4 [37.2 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.8-1 [1609 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5 [837 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9676 kB in 1s (8750 kB/s)
+Fetched 9676 kB in 1s (8339 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10788 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_powerpc.deb) ...
+(Reading database ... 10725 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_powerpc.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -243,7 +244,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.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.
@@ -272,11 +273,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 42 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 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_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-25-1 e2fsprogs_1.42~WIP-2011-09-25-1 fakeroot_1.18-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 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-13.11 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 libcomerr2_1.42~WIP-2011-09-25-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-09-25-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 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_3.0.0-4 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_1.3.3-15 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_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 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-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 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 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 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 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_5.9-2 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_1.2.0-4 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 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 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 │
@@ -287,12 +288,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -302,30 +303,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -338,21 +334,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -370,7 +366,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -430,10 +426,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -528,6 +520,13 @@ 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
@@ -603,7 +602,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -648,56 +647,56 @@ 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_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../bedtools_2.13.4-1_powerpc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../bedtools_2.14.2-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0309
+Build finished at 20111103-0353
-bedtools_2.13.4-1_powerpc.changes:
+bedtools_2.14.2-1_powerpc.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: powerpc
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org>
+Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- 530eb4bd481acaea490f723825e54eeee9f98404 593104 bedtools_2.13.4-1_powerpc.deb
+ 4a3f297f39976240e89d11e60ba6701ec48aa6c0 597052 bedtools_2.14.2-1_powerpc.deb
Checksums-Sha256:
- 9817df66bc57db8e4564d0df33e00a01fe307d0e2cf34605c4b557243721314d 593104 bedtools_2.13.4-1_powerpc.deb
+ 537a161c6461430e3545194e903c49744d6f7b129dd3067dea1c16b7422d77fa 597052 bedtools_2.14.2-1_powerpc.deb
Files:
- b7442900d5145a744cfc9457688086b9 593104 science optional bedtools_2.13.4-1_powerpc.deb
+ 319f9c3767930db8fdb8469c824e60a6 597052 science optional bedtools_2.14.2-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_powerpc.deb
+bedtools_2.14.2-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 593104 bytes: control archive= 1731 bytes.
+ size 597052 bytes: control archive= 1736 bytes.
867 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4841
+ Installed-Size: 4845
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
@@ -713,49 +712,49 @@ bedtools_2.13.4-1_powerpc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 03:09 ./
-drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/bin/
--rwxr-xr-x root/root 363104 2011-10-29 03:09 ./usr/bin/intersectBed
--rwxr-xr-x root/root 113948 2011-10-29 03:09 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 149868 2011-10-29 03:09 ./usr/bin/nucBed
--rwxr-xr-x root/root 63772 2011-10-29 03:09 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 133724 2011-10-29 03:09 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 125204 2011-10-29 03:09 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 113332 2011-10-29 03:09 ./usr/bin/mergeBed
--rwxr-xr-x root/root 301656 2011-10-29 03:09 ./usr/bin/windowBed
--rwxr-xr-x root/root 92620 2011-10-29 03:09 ./usr/bin/overlap
--rwxr-xr-x root/root 108772 2011-10-29 03:09 ./usr/bin/annotateBed
--rwxr-xr-x root/root 235964 2011-10-29 03:09 ./usr/bin/bamToBed
--rwxr-xr-x root/root 100652 2011-10-29 03:09 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 375408 2011-10-29 03:09 ./usr/bin/pairToBed
--rwxr-xr-x root/root 149860 2011-10-29 03:09 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 110972 2011-10-29 03:09 ./usr/bin/complementBed
--rwxr-xr-x root/root 125164 2011-10-29 03:09 ./usr/bin/closestBed
--rwxr-xr-x root/root 297552 2011-10-29 03:09 ./usr/bin/coverageBed
--rwxr-xr-x root/root 110324 2011-10-29 03:09 ./usr/bin/slopBed
--rwxr-xr-x root/root 174836 2011-10-29 03:09 ./usr/bin/pairToPair
--rwxr-xr-x root/root 318048 2011-10-29 03:09 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 240116 2011-10-29 03:09 ./usr/bin/bedToBam
--rwxr-xr-x root/root 314808 2011-10-29 03:09 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 109684 2011-10-29 03:09 ./usr/bin/linksBed
--rwxr-xr-x root/root 145636 2011-10-29 03:09 ./usr/bin/sortBed
--rwxr-xr-x root/root 115364 2011-10-29 03:09 ./usr/bin/subtractBed
--rwxr-xr-x root/root 117412 2011-10-29 03:09 ./usr/bin/flankBed
--rwxr-xr-x root/root 289608 2011-10-29 03:09 ./usr/bin/tagBam
-drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
-drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 03:05 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-03 03:52 ./
+drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/bin/
+-rwxr-xr-x root/root 149868 2011-11-03 03:52 ./usr/bin/nucBed
+-rwxr-xr-x root/root 363104 2011-11-03 03:52 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 113620 2011-11-03 03:52 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 145636 2011-11-03 03:52 ./usr/bin/sortBed
+-rwxr-xr-x root/root 240116 2011-11-03 03:52 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 125164 2011-11-03 03:52 ./usr/bin/closestBed
+-rwxr-xr-x root/root 314976 2011-11-03 03:52 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 109028 2011-11-03 03:52 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 149860 2011-11-03 03:52 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 111260 2011-11-03 03:52 ./usr/bin/complementBed
+-rwxr-xr-x root/root 375408 2011-11-03 03:52 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 297552 2011-11-03 03:52 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 101012 2011-11-03 03:52 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 110100 2011-11-03 03:52 ./usr/bin/linksBed
+-rwxr-xr-x root/root 110692 2011-11-03 03:52 ./usr/bin/slopBed
+-rwxr-xr-x root/root 115588 2011-11-03 03:52 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 301656 2011-11-03 03:52 ./usr/bin/windowBed
+-rwxr-xr-x root/root 235964 2011-11-03 03:52 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 289808 2011-11-03 03:52 ./usr/bin/tagBam
+-rwxr-xr-x root/root 133996 2011-11-03 03:52 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 63772 2011-11-03 03:52 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 175244 2011-11-03 03:52 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 125204 2011-11-03 03:52 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 318048 2011-11-03 03:52 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 117732 2011-11-03 03:52 ./usr/bin/flankBed
+-rwxr-xr-x root/root 114284 2011-11-03 03:52 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 92940 2011-11-03 03:52 ./usr/bin/overlap
+drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 03:47 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -769,7 +768,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-9ccd0ef2-1517-4631-b157-0cb77cbfd890/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-81e24f53-3bc3-46da-80f1-9a79708e877d/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -777,18 +776,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 105208
-Build-Time: 261
+Build-Space: 105644
+Build-Time: 306
Distribution: sid
-Install-Time: 61
-Job: bedtools_2.13.4-1
+Install-Time: 40
+Job: bedtools_2.14.2-1
Package: bedtools
-Package-Time: 364
-Source-Version: 2.13.4-1
-Space: 105208
+Package-Time: 390
+Source-Version: 2.14.2-1
+Space: 105644
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0309
-Build needed 00:06:04, 105208k disc space
-
+Finished at 20111103-0353
+Build needed 00:06:30, 105644k disc space
+Signature with key '6CB21D9F' requested:
diff --git a/s390.log b/s390.log
index 881a391..32cba12 100644
--- a/s390.log
+++ b/s390.log
@@ -1,4 +1,4 @@
-From buildd at zandonai.debian.org Sat Oct 29 04:48:27 2011
+From buildd at zandonai.debian.org Thu Nov 03 04:46:36 2011
Return-path: <buildd at zandonai.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,64 +6,64 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RK0qJ-0006yN-D1
- for logs at buildd.debian.org; Sat, 29 Oct 2011 04:48:27 +0000
+ id 1RLpCG-0003dn-9q
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:46:36 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RK0qI-00036v-JB; Sat, 29 Oct 2011 04:48:26 +0000
+ id 1RLpCF-0000Yf-Fo; Thu, 03 Nov 2011 04:46:35 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1RK0qI-0006qI-9M; Sat, 29 Oct 2011 04:48:26 +0000
-Message-Id: <E1RK0qI-0006qI-9M at zandonai.debian.org>
+ id 1RLpCE-0005Iq-6z; Thu, 03 Nov 2011 04:46:34 +0000
+Message-Id: <E1RLpCE-0005Iq-6z at zandonai.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 29 Oct 2011 04:48:26 +0000
+Date: Thu, 3 Nov 2011 04:46:34 +0000
From: buildd on zandonai <buildd at zandonai.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on s390 (dist=sid)
+Subject: Log for successful build of bedtools_2.14.2-1 on s390 (dist=sid)
Key-Id: 2D941D26
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (s390) 29 Oct 2011 04:44 ║
+║ bedtools 2.14.2-1 (s390) 03 Nov 2011 04:42 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: s390
Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.de.debian.org unstable/main Sources [5874 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5889 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5874 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [56.5 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [56.9 kB]
Get:7 http://ftp.de.debian.org unstable/non-free Sources [104 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7610 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.2 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7612 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.5 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7610 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.2 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7612 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.5 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [37.0 kB]
-Get:18 http://incoming.debian.org Packages [332 kB]
+Get:17 http://incoming.debian.org Sources [40.2 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.1 MB in 24s (1137 kB/s)
+Fetched 28.4 MB in 24s (1173 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 2s (461 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 1s (487 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -175,10 +175,10 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 41 not upgraded.
Need to get 9864 kB of archives.
After this operation, 28.0 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-3 [39.0 kB]
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-4 [38.9 kB]
Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
Get:3 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.8-1 [1681 kB]
Get:4 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-5 [879 kB]
@@ -200,10 +200,10 @@ Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.54-1 [28.4
Get:20 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9864 kB in 2s (3441 kB/s)
+Fetched 9864 kB in 2s (3419 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10631 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_s390.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_s390.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -244,7 +244,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.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.
@@ -273,11 +273,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
Toolchain package versions: binutils_2.21.90.20111004-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 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_4.6.1-13 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_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-05-2 e2fsprogs_1.42~WIP-2011-10-05-2 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 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-13.11 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 libcomerr2_1.42~WIP-2011-10-05-2 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-6 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-05-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 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_1.3.3-15 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_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 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_4.6.1-13 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_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-05-2 e2fsprogs_1.42~WIP-2011-10-05-2 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 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-13.11 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 libcomerr2_1.42~WIP-2011-10-05-2 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-6 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-05-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 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_1.3.3-15 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_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +288,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -309,24 +309,24 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-p
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -339,21 +339,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -529,6 +529,13 @@ 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
@@ -604,7 +611,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -649,22 +656,22 @@ 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_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.13.4-1_s390.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.14.2-1_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0448
+Build finished at 20111103-0446
-bedtools_2.13.4-1_s390.changes:
+bedtools_2.14.2-1_s390.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: s390
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -672,33 +679,33 @@ 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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- 5a423ec434d0e8494e2755a11c65c73c4f5a07c2 525452 bedtools_2.13.4-1_s390.deb
+ 0c593168e425781e7e31f78234990ffb23ee10c4 526928 bedtools_2.14.2-1_s390.deb
Checksums-Sha256:
- 7063b5d1a3abcd47378e8ba6a7d7c1dd03f7cdf75938fd3273babd57a1cbf801 525452 bedtools_2.13.4-1_s390.deb
+ 0d243a497531f0b00198351760cebfd017a113b194d92dcd980316f026c9be79 526928 bedtools_2.14.2-1_s390.deb
Files:
- 187fcb45404b6b106e22b00762fc49c3 525452 science optional bedtools_2.13.4-1_s390.deb
+ 5fdfeffb5d04e621414f595a4ca30852 526928 science optional bedtools_2.14.2-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_s390.deb
+bedtools_2.14.2-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 525452 bytes: control archive= 1732 bytes.
+ size 526928 bytes: control archive= 1739 bytes.
864 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4740
+ Installed-Size: 4749
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
@@ -714,49 +721,49 @@ bedtools_2.13.4-1_s390.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 04:48 ./
-drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/bin/
--rwxr-xr-x root/root 289044 2011-10-29 04:48 ./usr/bin/coverageBed
--rwxr-xr-x root/root 105796 2011-10-29 04:48 ./usr/bin/linksBed
--rwxr-xr-x root/root 293148 2011-10-29 04:48 ./usr/bin/windowBed
--rwxr-xr-x root/root 113560 2011-10-29 04:48 ./usr/bin/subtractBed
--rwxr-xr-x root/root 280868 2011-10-29 04:48 ./usr/bin/tagBam
--rwxr-xr-x root/root 114968 2011-10-29 04:48 ./usr/bin/flankBed
--rwxr-xr-x root/root 88452 2011-10-29 04:48 ./usr/bin/overlap
--rwxr-xr-x root/root 232524 2011-10-29 04:48 ./usr/bin/bamToBed
--rwxr-xr-x root/root 109648 2011-10-29 04:48 ./usr/bin/complementBed
--rwxr-xr-x root/root 305560 2011-10-29 04:48 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 112724 2011-10-29 04:48 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 145548 2011-10-29 04:48 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 63832 2011-10-29 04:48 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 371160 2011-10-29 04:48 ./usr/bin/pairToBed
--rwxr-xr-x root/root 235752 2011-10-29 04:48 ./usr/bin/bedToBam
--rwxr-xr-x root/root 97464 2011-10-29 04:48 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 109200 2011-10-29 04:48 ./usr/bin/mergeBed
--rwxr-xr-x root/root 122076 2011-10-29 04:48 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 176448 2011-10-29 04:48 ./usr/bin/pairToPair
--rwxr-xr-x root/root 104464 2011-10-29 04:48 ./usr/bin/annotateBed
--rwxr-xr-x root/root 133196 2011-10-29 04:48 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 145560 2011-10-29 04:48 ./usr/bin/nucBed
--rwxr-xr-x root/root 122384 2011-10-29 04:48 ./usr/bin/closestBed
--rwxr-xr-x root/root 309532 2011-10-29 04:48 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 358696 2011-10-29 04:48 ./usr/bin/intersectBed
--rwxr-xr-x root/root 145728 2011-10-29 04:48 ./usr/bin/sortBed
--rwxr-xr-x root/root 107056 2011-10-29 04:48 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 04:45 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-11-03 04:46 ./
+drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/
+drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/bin/
+-rwxr-xr-x root/root 289044 2011-11-03 04:46 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 106140 2011-11-03 04:46 ./usr/bin/linksBed
+-rwxr-xr-x root/root 293148 2011-11-03 04:46 ./usr/bin/windowBed
+-rwxr-xr-x root/root 114056 2011-11-03 04:46 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 280868 2011-11-03 04:46 ./usr/bin/tagBam
+-rwxr-xr-x root/root 116780 2011-11-03 04:46 ./usr/bin/flankBed
+-rwxr-xr-x root/root 88724 2011-11-03 04:46 ./usr/bin/overlap
+-rwxr-xr-x root/root 232524 2011-11-03 04:46 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 109912 2011-11-03 04:46 ./usr/bin/complementBed
+-rwxr-xr-x root/root 305840 2011-11-03 04:46 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 112724 2011-11-03 04:46 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 145548 2011-11-03 04:46 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 63832 2011-11-03 04:46 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 371648 2011-11-03 04:46 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 235752 2011-11-03 04:46 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 97800 2011-11-03 04:46 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 109472 2011-11-03 04:46 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 122412 2011-11-03 04:46 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 178220 2011-11-03 04:46 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 104652 2011-11-03 04:46 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 133196 2011-11-03 04:46 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 145560 2011-11-03 04:46 ./usr/bin/nucBed
+-rwxr-xr-x root/root 122760 2011-11-03 04:46 ./usr/bin/closestBed
+-rwxr-xr-x root/root 309532 2011-11-03 04:46 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 358696 2011-11-03 04:46 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 146224 2011-11-03 04:46 ./usr/bin/sortBed
+-rwxr-xr-x root/root 108588 2011-11-03 04:46 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 04:43 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -770,7 +777,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-5f182113-afe0-4fd0-9912-c4017f9968c8/build/buildd-bedtools_2.13.4-1-s390-7mfGTR
+Purging /var/lib/schroot/mount/sid-s390-sbuild-d3df2d3d-da7c-4ff3-a2d6-632bc0b5be2b/build/buildd-bedtools_2.14.2-1-s390-iHFiKc
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -778,18 +785,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 109412
-Build-Time: 170
+Build-Space: 110352
+Build-Time: 172
Distribution: sid
-Install-Time: 10
-Job: bedtools_2.13.4-1
+Install-Time: 9
+Job: bedtools_2.14.2-1
Package: bedtools
Package-Time: 218
-Source-Version: 2.13.4-1
-Space: 109412
+Source-Version: 2.14.2-1
+Space: 110352
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0448
-Build needed 00:03:38, 109412k disc space
+Finished at 20111103-0446
+Build needed 00:03:38, 110352k disc space
Signature with key '2D941D26' requested:
diff --git a/sparc.log b/sparc.log
index bfe1c94..cbe1c26 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,69 +1,70 @@
-From buildd at lebrun.debian.org Sat Oct 29 04:42:32 2011
-Return-path: <buildd at lebrun.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at schroeder.debian.org Thu Nov 03 04:11:58 2011
+Return-path: <buildd at schroeder.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1RK0ka-0006LI-DL
- for logs at buildd.debian.org; Sat, 29 Oct 2011 04:42:32 +0000
-Received: from lebrun.debian.org ([193.198.184.10])
+ (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
+ id 1RLoek-0006q6-Oz
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:11:58 +0000
+Received: from schroeder.debian.org ([193.198.184.11])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1RK0kZ-0002sp-J8
- for logs at buildd.debian.org; Sat, 29 Oct 2011 04:42:31 +0000
-Received: from buildd by lebrun.debian.org with local (Exim 4.72)
- (envelope-from <buildd at lebrun.debian.org>)
- id 1RK0kX-0006eR-IR; Sat, 29 Oct 2011 04:42:29 +0000
-Message-Id: <E1RK0kX-0006eR-IR at lebrun.debian.org>
+ CN=schroeder.debian.org,
+ EMAIL=hostmaster at schroeder.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
+ id 1RLoek-0003dU-47
+ for logs at buildd.debian.org; Thu, 03 Nov 2011 04:11:58 +0000
+Received: from buildd by schroeder.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at schroeder.debian.org>)
+ id 1RLoei-0004Be-Hs; Thu, 03 Nov 2011 04:11:56 +0000
+Message-Id: <E1RLoei-0004Be-Hs at schroeder.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 29 Oct 2011 04:42:29 +0000
-From: buildd on lebrun <buildd at lebrun.debian.org>
-To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
-Subject: Log for successful build of bedtools_2.13.4-1 on sparc (dist=sid)
-Key-Id: 632E3DB6
+Date: Thu, 3 Nov 2011 04:11:56 +0000
+From: buildd on schroeder <buildd at schroeder.debian.org>
+To: logs at buildd.debian.org,buildd-admin at schroeder.debian.org
+Subject: Log for successful build of bedtools_2.14.2-1 on sparc (dist=sid)
+Key-Id: 7C392B18
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.4-1 (sparc) 29 Oct 2011 04:30 ║
+║ bedtools 2.14.2-1 (sparc) 03 Nov 2011 03:59 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.4-1
-Source Version: 2.13.4-1
+Version: 2.14.2-1
+Source Version: 2.14.2-1
Architecture: sparc
-Get:1 http://debian.carnet.hr unstable InRelease [146 kB]
+Get:1 http://ftp.hr.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://debian.carnet.hr unstable/main Sources [5874 kB]
-Get:4 http://debian.carnet.hr unstable/contrib Sources [56.5 kB]
-Get:5 http://debian.carnet.hr unstable/non-free Sources [104 kB]
-Get:6 http://debian.carnet.hr unstable/main sparc Packages [7644 kB]
+Get:3 http://ftp.hr.debian.org unstable/main Sources [5889 kB]
+Get:4 http://ftp.hr.debian.org unstable/contrib Sources [56.9 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org Release [1604 B]
-Get:9 http://incoming.debian.org unstable/main Sources [5874 kB]
-Get:10 http://debian.carnet.hr unstable/contrib sparc Packages [55.3 kB]
-Ign http://debian.carnet.hr unstable/contrib TranslationIndex
-Get:11 http://debian.carnet.hr unstable/main TranslationIndex [2045 B]
-Ign http://debian.carnet.hr unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:5 http://incoming.debian.org Release.gpg [836 B]
+Get:6 http://ftp.hr.debian.org unstable/non-free Sources [104 kB]
+Get:7 http://incoming.debian.org Release [1604 B]
+Get:8 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:9 http://ftp.hr.debian.org unstable/main sparc Packages [7651 kB]
+Get:10 http://ftp.hr.debian.org unstable/contrib sparc Packages [55.5 kB]
+Ign http://ftp.hr.debian.org unstable/contrib TranslationIndex
+Get:11 http://ftp.hr.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.hr.debian.org unstable/contrib Translation-en
+Get:12 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
Get:13 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:14 http://incoming.debian.org unstable/main sparc Packages [7644 kB]
-Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.3 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7652 kB]
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.5 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [36.6 kB]
-Get:18 http://incoming.debian.org Packages [333 kB]
+Get:17 http://incoming.debian.org Sources [40.9 kB]
+Get:18 http://incoming.debian.org Packages [602 kB]
Ign http://incoming.debian.org Translation-en
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 28.1 MB in 29s (945 kB/s)
+Fetched 28.5 MB in 33s (846 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +85,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 922 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
-Fetched 922 kB in 2s (389 kB/s)
+Need to get 928 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Fetched 928 kB in 2s (397 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +109,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -128,9 +129,9 @@ bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
+diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b2)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
@@ -176,35 +177,35 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.
-Need to get 9455 kB of archives.
+0 upgraded, 21 newly installed, 0 to remove and 15 not upgraded.
+Need to get 9454 kB of archives.
After this operation, 27.2 MB of additional disk space will be used.
-Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
-Get:2 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
-Get:3 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.8-1 [1508 kB]
-Get:4 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5 [816 kB]
-Get:5 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
-Get:6 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
-Get:7 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:8 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:9 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
-Get:10 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
-Get:11 http://debian.carnet.hr/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
-Get:12 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
-Get:13 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:15 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
-Get:16 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
-Get:20 http://debian.carnet.hr/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+Get:1 http://ftp.hr.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.0-4 [34.9 kB]
+Get:2 http://ftp.hr.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
+Get:3 http://ftp.hr.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.28.8-1 [1508 kB]
+Get:4 http://ftp.hr.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5 [816 kB]
+Get:5 http://ftp.hr.debian.org/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
+Get:6 http://ftp.hr.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:7 http://ftp.hr.debian.org/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:8 http://ftp.hr.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:9 http://ftp.hr.debian.org/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
+Get:10 http://ftp.hr.debian.org/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
+Get:11 http://ftp.hr.debian.org/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
+Get:12 http://ftp.hr.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
+Get:13 http://ftp.hr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://ftp.hr.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:15 http://ftp.hr.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
+Get:16 http://ftp.hr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://ftp.hr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://ftp.hr.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://ftp.hr.debian.org/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
+Get:20 http://ftp.hr.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://ftp.hr.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9455 kB in 8s (1135 kB/s)
+Fetched 9454 kB in 8s (1162 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10908 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_sparc.deb) ...
+(Reading database ... 10913 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_sparc.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
Selecting previously unselected package libglib2.0-0.
@@ -245,7 +246,7 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.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.
@@ -274,11 +275,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_2.21.90.20111004-2 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_4.6.1-15 dash_0.5.7-2 debconf_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_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b2 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 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 libc6-dev-sparc64_2.13-21 libc6-sparc64_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 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_1.3.3-15+b1 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 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_4.6.2-1 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 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+b2 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 libc6-dev-sparc64_2.13-21 libc6-sparc64_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 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 libgomp1_4.6.2-1 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_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-3 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -289,12 +290,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./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: failed to verify signature on ./bedtools_2.14.2-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.2
+dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -305,24 +306,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.4-1
- dpkg-source --before-build bedtools-2.13.4
+dpkg-buildpackage: source version 2.14.2-1
+ dpkg-source --before-build bedtools-2.14.2
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -335,21 +336,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -521,6 +522,13 @@ 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
@@ -596,7 +604,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -641,56 +649,56 @@ 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_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bedtools_2.13.4-1_sparc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org> >../bedtools_2.14.2-1_sparc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.4
+ dpkg-source --after-build bedtools-2.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111029-0442
+Build finished at 20111103-0411
-bedtools_2.13.4-1_sparc.changes:
+bedtools_2.14.2-1_sparc.changes:
Format: 1.8
-Date: Sat, 29 Oct 2011 11:08:02 +0900
+Date: Thu, 03 Nov 2011 12:15:32 +0900
Source: bedtools
Binary: bedtools
Architecture: sparc
-Version: 2.13.4-1
+Version: 2.14.2-1
Distribution: sid
Urgency: low
-Maintainer: sparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org>
+Maintainer: sparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org>
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 (2.14.2-1) unstable; urgency=low
.
- [e553c37] New upstream release.
+ [356313d] Bugfix release.
Checksums-Sha1:
- 13a45b7ece651e91bd674aaf50200938d5550af4 566770 bedtools_2.13.4-1_sparc.deb
+ 592e74505b07a85fdfeb12a91f53ea9dbb7f5f12 569290 bedtools_2.14.2-1_sparc.deb
Checksums-Sha256:
- 5d69b4719e0747483606d8cef7f20c0830f6fbffa3b0b11c318a0754c237ca03 566770 bedtools_2.13.4-1_sparc.deb
+ f43e599ad33f7a494758aa6110f7e76f4d858b990efc6f01a4fd919b0780967b 569290 bedtools_2.14.2-1_sparc.deb
Files:
- 22f3cca102d26fa103651de3acc9a083 566770 science optional bedtools_2.13.4-1_sparc.deb
+ f98a2c510f45c02ba5b1d477d5b1dd9f 569290 science optional bedtools_2.14.2-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.4-1_sparc.deb
+bedtools_2.14.2-1_sparc.deb
───────────────────────────
new debian package, version 2.0.
- size 566770 bytes: control archive= 1729 bytes.
+ size 569290 bytes: control archive= 1733 bytes.
865 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.4-1
+ Version: 2.14.2-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4594
+ Installed-Size: 4589
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.6), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -706,49 +714,49 @@ bedtools_2.13.4-1_sparc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-29 04:41 ./
-drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/
-drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/bin/
--rwxr-xr-x root/root 298604 2011-10-29 04:41 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 293484 2011-10-29 04:41 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 103412 2011-10-29 04:41 ./usr/bin/complementBed
--rwxr-xr-x root/root 175004 2011-10-29 04:41 ./usr/bin/pairToPair
--rwxr-xr-x root/root 274036 2011-10-29 04:41 ./usr/bin/tagBam
--rwxr-xr-x root/root 142564 2011-10-29 04:41 ./usr/bin/nucBed
--rwxr-xr-x root/root 282188 2011-10-29 04:41 ./usr/bin/windowBed
--rwxr-xr-x root/root 142528 2011-10-29 04:41 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 109568 2011-10-29 04:41 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 60340 2011-10-29 04:41 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 347776 2011-10-29 04:41 ./usr/bin/intersectBed
--rwxr-xr-x root/root 102840 2011-10-29 04:41 ./usr/bin/slopBed
--rwxr-xr-x root/root 110056 2011-10-29 04:41 ./usr/bin/subtractBed
--rwxr-xr-x root/root 119044 2011-10-29 04:41 ./usr/bin/closestBed
--rwxr-xr-x root/root 106176 2011-10-29 04:41 ./usr/bin/mergeBed
--rwxr-xr-x root/root 117984 2011-10-29 04:41 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 364188 2011-10-29 04:41 ./usr/bin/pairToBed
--rwxr-xr-x root/root 94192 2011-10-29 04:41 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 127536 2011-10-29 04:41 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 104252 2011-10-29 04:41 ./usr/bin/linksBed
--rwxr-xr-x root/root 84868 2011-10-29 04:41 ./usr/bin/overlap
--rwxr-xr-x root/root 278172 2011-10-29 04:41 ./usr/bin/coverageBed
--rwxr-xr-x root/root 144116 2011-10-29 04:41 ./usr/bin/sortBed
--rwxr-xr-x root/root 224720 2011-10-29 04:41 ./usr/bin/bamToBed
--rwxr-xr-x root/root 101708 2011-10-29 04:41 ./usr/bin/annotateBed
--rwxr-xr-x root/root 110716 2011-10-29 04:41 ./usr/bin/flankBed
--rwxr-xr-x root/root 224712 2011-10-29 04:41 ./usr/bin/bedToBam
-drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-29 04:32 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-03 04:11 ./
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+-rwxr-xr-x root/root 109568 2011-11-03 04:11 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 60340 2011-11-03 04:11 ./usr/bin/unionBedGraphs
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+-rwxr-xr-x root/root 118900 2011-11-03 04:11 ./usr/bin/closestBed
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+-rwxr-xr-x root/root 117776 2011-11-03 04:11 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 293276 2011-11-03 04:11 ./usr/bin/genomeCoverageBed
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+-rwxr-xr-x root/root 104044 2011-11-03 04:11 ./usr/bin/linksBed
+-rwxr-xr-x root/root 298604 2011-11-03 04:11 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 277964 2011-11-03 04:11 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 224712 2011-11-03 04:11 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 84868 2011-11-03 04:11 ./usr/bin/overlap
+-rwxr-xr-x root/root 282188 2011-11-03 04:11 ./usr/bin/windowBed
+-rwxr-xr-x root/root 364188 2011-11-03 04:11 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 143908 2011-11-03 04:11 ./usr/bin/sortBed
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+-rwxr-xr-x root/root 347776 2011-11-03 04:11 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 101500 2011-11-03 04:11 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 109848 2011-11-03 04:11 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 142564 2011-11-03 04:11 ./usr/bin/nucBed
+-rwxr-xr-x root/root 175004 2011-11-03 04:11 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 102632 2011-11-03 04:11 ./usr/bin/slopBed
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+-rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-11-03 04:11 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-03 04:01 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -762,7 +770,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-91ac1074-8b93-44eb-820f-cfc94961ab24/build/buildd-bedtools_2.13.4-1-sparc-1fdoun
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-0fa400a1-bc41-4822-819d-a988d8aa4b9e/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -770,18 +778,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 101744
-Build-Time: 615
+Build-Space: 102596
+Build-Time: 628
Distribution: sid
-Install-Time: 65
-Job: bedtools_2.13.4-1
+Install-Time: 56
+Job: bedtools_2.14.2-1
Package: bedtools
-Package-Time: 735
-Source-Version: 2.13.4-1
-Space: 101744
+Package-Time: 739
+Source-Version: 2.14.2-1
+Space: 102596
Status: successful
-Version: 2.13.4-1
+Version: 2.14.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111029-0442
-Build needed 00:12:15, 101744k disc space
-Signature with key '632E3DB6' requested:
+Finished at 20111103-0411
+Build needed 00:12:19, 102596k disc space
+Signature with key '7C392B18' requested:
--
Suite of utilities for comparing genomic features.
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