This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch experimental-meta in repository bwa.
commit dd91a504da63f53b673affa2598cfd247ad14636 Author: Charles Plessy <[email protected]> Date: Sat Jul 4 13:12:31 2015 +0900 Logs for 0.7.12-1 on kfreebsd-amd64. --- info | 12 +- kfreebsd-amd64.log | 888 +++++++++++++++++++++++++---------------------------- 2 files changed, 420 insertions(+), 480 deletions(-) diff --git a/info b/info index 5c74a5b..e216ec9 100644 --- a/info +++ b/info @@ -1,11 +1 @@ -i386~1321931904~experimental~successful -kfreebsd-i386~1321932065~experimental~successful -ia64~1321932088~experimental~successful -kfreebsd-amd64~1321932111~experimental~successful -powerpc~1321932119~experimental~successful -armel~1321932274~experimental~successful -mipsel~1321932318~experimental~successful -s390~1321932380~experimental~successful -mips~1321932524~experimental~successful -hurd-i386~1321952627~experimental~successful -sparc~1321954799~experimental~successful +kfreebsd-amd64~1422548992~experimental~failed diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log index 66eb4d2..cda1d1f 100644 --- a/kfreebsd-amd64.log +++ b/kfreebsd-amd64.log @@ -1,122 +1,92 @@ -From [email protected] Tue Nov 22 03:21:50 2011 +From [email protected] Thu Jan 29 16:29:52 2015 Return-path: <[email protected]> -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 protected] (verified) - by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) - (Exim 4.72) (envelope-from <[email protected]>) - id 1RSgve-0006Fa-Gp - for [email protected]; Tue, 22 Nov 2011 03:21:50 +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 protected] (verified) - by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) - (Exim 4.72) (envelope-from <[email protected]>) - id 1RSgvd-0001YA-9b; Tue, 22 Nov 2011 03:21:50 +0000 -Received: from buildd by fano.debian.org with local (Exim 4.72) - (envelope-from <[email protected]>) - id 1RSgvX-000LeO-Bs; Tue, 22 Nov 2011 03:21:43 +0000 -Message-Id: <[email protected]> -MIME-Version: 1.0 +Received: from muffat.debian.org ([2607:f8f0:610:4000:6564:a62:ce0c:1392]) + from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, + CN=muffat.debian.org, [email protected] (verified) + by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128) + (Exim 4.80) (envelope-from <[email protected]>) + id 1YGryZ-000097-Rq + for [email protected]; Thu, 29 Jan 2015 16:29:52 +0000 +Received: from fano.debian.org ([2607:f8f0:610:4000:6564:a62:19:110]) + from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, + CN=fano.debian.org, [email protected] (verified) + by muffat.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128) + (Exim 4.80) (envelope-from <[email protected]>) + id 1YGryX-0006Ho-8V; Thu, 29 Jan 2015 16:29:49 +0000 +Received: from buildd by fano.debian.org with local (Exim 4.80) + (envelope-from <[email protected]>) + id 1YGryW-000Cei-Sl; Thu, 29 Jan 2015 16:29:48 +0000 Content-Transfer-Encoding: binary -X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08) -Date: Tue, 22 Nov 2011 03:21:43 +0000 +MIME-Version: 1.0 +X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13) +Date: Thu, 29 Jan 2015 16:29:48 +0000 From: buildd on fano <[email protected]> -To: [email protected],[email protected],[email protected] -Subject: Log for successful build of bwa_0.6.0-2 on kfreebsd-amd64 - (dist=experimental) -Key-Id: D33FE1D8 +To: [email protected],[email protected] +Subject: Log for attempted build of bwa_0.7.12-1 on kfreebsd-amd64 + (dist=experimental) +Key-Id: 8C5D26F3 +Message-Id: <[email protected]> Delivered-To: [email protected] -sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org +sbuild (Debian sbuild) 0.64.0 (17 May 2013) on fano.debian.org ╔══════════════════════════════════════════════════════════════════════════════╗ -║ bwa 0.6.0-2 (kfreebsd-amd64) 22 Nov 2011 03:19 ║ +║ bwa 0.7.12-1 (kfreebsd-amd64) 29 Jan 2015 16:27 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: bwa -Version: 0.6.0-2 -Source Version: 0.6.0-2 -Architecture: kfreebsd-amd64 -Get:1 http://incoming.debian.org sid InRelease [160 kB] -Get:2 http://mirror-ubc.debian.org sid InRelease [160 kB] -Get:3 http://mirror-ubc.debian.org experimental InRelease [139 kB] -Get:4 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B] -Ign http://incoming.debian.org InRelease -Get:5 http://incoming.debian.org experimental InRelease [139 kB] -Ign http://incoming.debian.org InRelease -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:6 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B] -Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex -Get:7 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-21-2017.26.pdiff [13.6 kB] -Get:8 http://mirror-ubc.debian.org experimental/main Sources/DiffIndex [2023 B] -Hit http://mirror-ubc.debian.org experimental/contrib Sources/DiffIndex -Hit http://mirror-ubc.debian.org experimental/non-free Sources/DiffIndex -Get:9 http://mirror-ubc.debian.org experimental/main kfreebsd-amd64 Packages/DiffIndex [2023 B] -Hit http://mirror-ubc.debian.org experimental/contrib kfreebsd-amd64 Packages/DiffIndex -Hit http://mirror-ubc.debian.org experimental/non-free kfreebsd-amd64 Packages/DiffIndex -Ign http://mirror-ubc.debian.org experimental/contrib TranslationIndex -Ign http://mirror-ubc.debian.org experimental/main TranslationIndex -Ign http://mirror-ubc.debian.org experimental/non-free TranslationIndex -Get:10 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-21-2017.26.pdiff [13.6 kB] -Get:11 http://incoming.debian.org Release.gpg [836 B] -Get:12 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [84.5 kB] -Get:13 http://mirror-ubc.debian.org experimental/main 2011-11-21-2017.26.pdiff [1146 B] -Get:14 http://mirror-ubc.debian.org experimental/main kfreebsd-amd64 2011-11-21-2017.26.pdiff [3146 B] -Get:15 http://mirror-ubc.debian.org experimental/non-free kfreebsd-amd64 Packages [4360 B] -Get:16 http://incoming.debian.org Release.gpg [836 B] -Get:17 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B] -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 -Get:18 http://incoming.debian.org sid/main TranslationIndex [2045 B] -Ign http://incoming.debian.org sid/non-free TranslationIndex -Get:19 http://incoming.debian.org experimental/main Sources/DiffIndex [2023 B] -Hit http://incoming.debian.org experimental/contrib Sources/DiffIndex -Hit http://incoming.debian.org experimental/non-free Sources/DiffIndex -Get:20 http://mirror-ubc.debian.org experimental/main 2011-11-21-2017.26.pdiff [1146 B] -Get:21 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-22-0216.01.pdiff [11.9 kB] -Get:22 http://mirror-ubc.debian.org experimental/main kfreebsd-amd64 2011-11-21-2017.26.pdiff [3146 B] -Get:23 http://mirror-ubc.debian.org experimental/main 2011-11-22-0216.01.pdiff [990 B] -Ign http://mirror-ubc.debian.org sid/contrib Translation-en -Ign http://mirror-ubc.debian.org sid/non-free Translation-en -Ign http://mirror-ubc.debian.org experimental/contrib Translation-en -Ign http://mirror-ubc.debian.org experimental/main Translation-en -Ign http://mirror-ubc.debian.org experimental/non-free Translation-en -Get:24 http://incoming.debian.org experimental/main kfreebsd-amd64 Packages/DiffIndex [2023 B] -Hit http://incoming.debian.org experimental/contrib kfreebsd-amd64 Packages/DiffIndex -Get:25 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-22-0216.01.pdiff [11.9 kB] -Get:26 http://mirror-ubc.debian.org experimental/main kfreebsd-amd64 2011-11-22-0216.01.pdiff [3039 B] -Hit http://incoming.debian.org experimental/non-free kfreebsd-amd64 Packages/DiffIndex -Ign http://incoming.debian.org experimental/contrib TranslationIndex -Ign http://incoming.debian.org experimental/main TranslationIndex -Ign http://incoming.debian.org experimental/non-free TranslationIndex -Get:27 http://incoming.debian.org Release [1604 B] -Get:28 http://incoming.debian.org Release [1626 B] -Get:29 http://incoming.debian.org sid/main kfreebsd-amd64 2011-11-22-0216.01.pdiff [11.9 kB] -Get:30 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [84.5 kB] -Get:31 http://incoming.debian.org experimental/main 2011-11-22-0216.01.pdiff [990 B] -Get:32 http://incoming.debian.org experimental/main kfreebsd-amd64 2011-11-22-0216.01.pdiff [3039 B] -Get:33 http://incoming.debian.org experimental/non-free kfreebsd-amd64 Packages [4360 B] -Get:34 http://incoming.debian.org Packages [315 kB] -Get:35 http://incoming.debian.org Sources [2999 B] -Get:36 http://incoming.debian.org Packages [28.9 kB] -Get:37 http://mirror-ubc.debian.org experimental/main 2011-11-22-0216.01.pdiff [990 B] -Get:38 http://mirror-ubc.debian.org experimental/main kfreebsd-amd64 2011-11-22-0216.01.pdiff [3039 B] -Get:39 http://incoming.debian.org sid/main kfreebsd-amd64 2011-11-22-0216.01.pdiff [11.9 kB] -Ign http://incoming.debian.org sid/contrib Translation-en -Ign http://incoming.debian.org sid/non-free Translation-en -Ign http://incoming.debian.org experimental/contrib Translation-en -Ign http://incoming.debian.org experimental/main Translation-en -Ign http://incoming.debian.org experimental/non-free Translation-en -Ign http://incoming.debian.org Translation-en -Ign http://incoming.debian.org Translation-en -Get:40 http://incoming.debian.org experimental/main 2011-11-22-0216.01.pdiff [990 B] -Get:41 http://incoming.debian.org experimental/main kfreebsd-amd64 2011-11-22-0216.01.pdiff [3039 B] -Fetched 1194 kB in 9s (129 kB/s) +Version: 0.7.12-1 +Source Version: 0.7.12-1 +Distribution: experimental +Machine Architecture: kfreebsd-amd64 +Host Architecture: kfreebsd-amd64 +Build Architecture: kfreebsd-amd64 + +I: NOTICE: Log filtering will replace 'build/bwa-Ac81kN/bwa-0.7.12' with '«PKGBUILDDIR»' +I: NOTICE: Log filtering will replace 'build/bwa-Ac81kN' with '«BUILDDIR»' +I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-experimental-ka-sbuild-1422548873-47431' with '«CHROOT»' + +┌──────────────────────────────────────────────────────────────────────────────┐ +│ Update chroot │ +└──────────────────────────────────────────────────────────────────────────────┘ + +Get:1 http://mirror-ubc.debian.org unstable InRelease [249 kB] +Get:2 http://mirror-ubc.debian.org experimental InRelease [162 kB] +Get:3 http://mirror-ubc.debian.org unstable/main Sources [9853 kB] +Get:4 http://ftp.debian.org unstable InRelease [249 kB] +Get:5 http://incoming.debian.org buildd-unstable InRelease [110 kB] +Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [66.6 kB] +Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [125 kB] +Get:8 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [8806 kB] +Get:9 http://incoming.debian.org buildd-experimental InRelease [110 kB] +Get:10 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [46.6 kB] +Get:11 http://mirror-ubc.debian.org experimental/main Sources [918 kB] +Get:12 http://mirror-ubc.debian.org experimental/contrib Sources [5636 B] +Get:13 http://mirror-ubc.debian.org experimental/non-free Sources [6263 B] +Get:14 http://ftp.debian.org experimental InRelease [162 kB] +Get:15 http://incoming.debian.org buildd-unstable/main Sources [44.1 kB] +Get:16 http://mirror-ubc.debian.org experimental/main kfreebsd-amd64 Packages [1107 kB] +Get:17 http://mirror-ubc.debian.org experimental/contrib kfreebsd-amd64 Packages [6602 B] +Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [20 B] +Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [20 B] +Get:20 http://ftp.debian.org unstable/main Sources [9853 kB] +Get:21 http://incoming.debian.org buildd-unstable/main kfreebsd-amd64 Packages [44.9 kB] +Get:22 http://incoming.debian.org buildd-unstable/contrib kfreebsd-amd64 Packages [481 B] +Get:23 http://incoming.debian.org buildd-experimental/main Sources [28.1 kB] +Get:24 http://incoming.debian.org buildd-experimental/contrib Sources [20 B] +Get:25 http://incoming.debian.org buildd-experimental/non-free Sources [20 B] +Get:26 http://incoming.debian.org buildd-experimental/main kfreebsd-amd64 Packages [28.9 kB] +Get:27 http://incoming.debian.org buildd-experimental/contrib kfreebsd-amd64 Packages [20 B] +Get:28 http://ftp.debian.org unstable/contrib Sources [66.6 kB] +Get:29 http://ftp.debian.org unstable/non-free Sources [125 kB] +Get:30 http://ftp.debian.org unstable/main kfreebsd-amd64 Packages [8806 kB] +Get:31 http://ftp.debian.org unstable/contrib kfreebsd-amd64 Packages [46.6 kB] +Get:32 http://ftp.debian.org experimental/main Sources [918 kB] +Get:33 http://ftp.debian.org experimental/contrib Sources [5636 B] +Get:34 http://ftp.debian.org experimental/non-free Sources [6263 B] +Get:35 http://ftp.debian.org experimental/main kfreebsd-amd64 Packages [1107 kB] +Get:36 http://ftp.debian.org experimental/contrib kfreebsd-amd64 Packages [6602 B] +Fetched 43.1 MB in 14s (2974 kB/s) Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ @@ -136,17 +106,20 @@ Reading package lists... Building dependency tree... Reading state information... NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at: -git://git.debian.org/debian-med/bwa.git -Need to get 171 kB of source archives. -Get:1 http://incoming.debian.org/buildd-experimental/ bwa 0.6.0-2 (dsc) [1681 B] -Get:2 http://incoming.debian.org/buildd-experimental/ bwa 0.6.0-2 (tar) [169 kB] -Fetched 171 kB in 0s (234 kB/s) +git://anonscm.debian.org/debian-med/bwa.git +Need to get 193 kB of source archives. +Get:1 http://mirror-ubc.debian.org/debian/ experimental/main bwa 0.7.12-1 (dsc) [2013 B] +Get:2 http://mirror-ubc.debian.org/debian/ experimental/main bwa 0.7.12-1 (tar) [185 kB] +Get:3 http://mirror-ubc.debian.org/debian/ experimental/main bwa 0.7.12-1 (diff) [5956 B] +Fetched 193 kB in 0s (2951 kB/s) Download complete and in download only mode Check arch ────────── -dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi/resolver-xBK753/apt_archive/sbuild-build-depends-core-dummy.deb'. +Merged Build-Depends: build-essential, fakeroot +Filtered Build-Depends: build-essential, fakeroot +dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-vEJtTq/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... @@ -157,24 +130,95 @@ Reading package lists... Reading package lists... Building dependency tree... Reading state information... -aptitude is already the newest version. -0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. +The following extra packages will be installed: + aptitude-common libboost-iostreams1.55.0 libcwidget3 libncurses5 + libncursesw5 libsigc++-2.0-0c2a libsqlite3-0 libtinfo5 libxapian22 +Suggested packages: + tasksel debtags apt-xapian-index libcwidget-dev xapian-tools +Recommended packages: + aptitude-doc-en aptitude-doc libparse-debianchangelog-perl +The following NEW packages will be installed: + aptitude aptitude-common libboost-iostreams1.55.0 libcwidget3 libncursesw5 + libsigc++-2.0-0c2a libsqlite3-0 libxapian22 +The following packages will be upgraded: + libncurses5 libtinfo5 +2 upgraded, 8 newly installed, 0 to remove and 80 not upgraded. +Need to get 5327 kB of archives. +After this operation, 21.9 MB of additional disk space will be used. +Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 kfreebsd-amd64 5.9+20140913-1+b1 [282 kB] +Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 kfreebsd-amd64 5.9+20140913-1+b1 [95.8 kB] +Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libboost-iostreams1.55.0 kfreebsd-amd64 1.55.0+dfsg-3 [49.4 kB] +Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libncursesw5 kfreebsd-amd64 5.9+20140913-1+b1 [122 kB] +Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libsigc++-2.0-0c2a kfreebsd-amd64 2.4.0-1 [51.0 kB] +Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libcwidget3 kfreebsd-amd64 0.5.17-2 [349 kB] +Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libsqlite3-0 kfreebsd-amd64 3.8.7.4-1 [437 kB] +Get:8 http://mirror-ubc.debian.org/debian/ unstable/main aptitude-common all 0.6.11-1 [1576 kB] +Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxapian22 kfreebsd-amd64 1.2.19-1 [984 kB] +Get:10 http://mirror-ubc.debian.org/debian/ unstable/main aptitude kfreebsd-amd64 0.6.11-1+b1 [1381 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 5327 kB in 0s (21.4 MB/s) +(Reading database ... 11502 files and directories currently installed.) +Preparing to unpack .../libtinfo5_5.9+20140913-1+b1_kfreebsd-amd64.deb ... +Unpacking libtinfo5:kfreebsd-amd64 (5.9+20140913-1+b1) over (5.9+20140913-1) ... +Setting up libtinfo5:kfreebsd-amd64 (5.9+20140913-1+b1) ... +Processing triggers for libc-bin (2.19-12) ... +(Reading database ... 11503 files and directories currently installed.) +Preparing to unpack .../libncurses5_5.9+20140913-1+b1_kfreebsd-amd64.deb ... +Unpacking libncurses5:kfreebsd-amd64 (5.9+20140913-1+b1) over (5.9+20140913-1) ... +Setting up libncurses5:kfreebsd-amd64 (5.9+20140913-1+b1) ... +Processing triggers for libc-bin (2.19-12) ... +Selecting previously unselected package libboost-iostreams1.55.0:kfreebsd-amd64. +(Reading database ... 11503 files and directories currently installed.) +Preparing to unpack .../libboost-iostreams1.55.0_1.55.0+dfsg-3_kfreebsd-amd64.deb ... +Unpacking libboost-iostreams1.55.0:kfreebsd-amd64 (1.55.0+dfsg-3) ... +Selecting previously unselected package libncursesw5:kfreebsd-amd64. +Preparing to unpack .../libncursesw5_5.9+20140913-1+b1_kfreebsd-amd64.deb ... +Unpacking libncursesw5:kfreebsd-amd64 (5.9+20140913-1+b1) ... +Selecting previously unselected package libsigc++-2.0-0c2a:kfreebsd-amd64. +Preparing to unpack .../libsigc++-2.0-0c2a_2.4.0-1_kfreebsd-amd64.deb ... +Unpacking libsigc++-2.0-0c2a:kfreebsd-amd64 (2.4.0-1) ... +Selecting previously unselected package libcwidget3:kfreebsd-amd64. +Preparing to unpack .../libcwidget3_0.5.17-2_kfreebsd-amd64.deb ... +Unpacking libcwidget3:kfreebsd-amd64 (0.5.17-2) ... +Selecting previously unselected package libsqlite3-0:kfreebsd-amd64. +Preparing to unpack .../libsqlite3-0_3.8.7.4-1_kfreebsd-amd64.deb ... +Unpacking libsqlite3-0:kfreebsd-amd64 (3.8.7.4-1) ... +Selecting previously unselected package aptitude-common. +Preparing to unpack .../aptitude-common_0.6.11-1_all.deb ... +Unpacking aptitude-common (0.6.11-1) ... +Selecting previously unselected package libxapian22. +Preparing to unpack .../libxapian22_1.2.19-1_kfreebsd-amd64.deb ... +Unpacking libxapian22 (1.2.19-1) ... +Selecting previously unselected package aptitude. +Preparing to unpack .../aptitude_0.6.11-1+b1_kfreebsd-amd64.deb ... +Unpacking aptitude (0.6.11-1+b1) ... +Setting up libboost-iostreams1.55.0:kfreebsd-amd64 (1.55.0+dfsg-3) ... +Setting up libncursesw5:kfreebsd-amd64 (5.9+20140913-1+b1) ... +Setting up libsigc++-2.0-0c2a:kfreebsd-amd64 (2.4.0-1) ... +Setting up libcwidget3:kfreebsd-amd64 (0.5.17-2) ... +Setting up libsqlite3-0:kfreebsd-amd64 (3.8.7.4-1) ... +Setting up aptitude-common (0.6.11-1) ... +Setting up libxapian22 (1.2.19-1) ... +Setting up aptitude (0.6.11-1+b1) ... +update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode +Processing triggers for libc-bin (2.19-12) ... aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-core-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-core-dummy Reading package lists... Building dependency tree... Reading state information... -Reading extended state information... Initializing package states... Writing extended state information... +Building tag database... The following NEW packages will be installed: sbuild-build-depends-core-dummy -0 packages upgraded, 1 newly installed, 0 to remove and 2 not upgraded. -Need to get 0 B/714 B of archives. After unpacking 0 B will be used. +0 packages upgraded, 1 newly installed, 0 to remove and 80 not upgraded. +Need to get 0 B/828 B of archives. After unpacking 0 B will be used. Writing extended state information... debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sbuild-build-depends-core-dummy. -(Reading database ... 12474 files and directories currently installed.) -Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... +(Reading database ... 11758 files and directories currently installed.) +Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... +Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... @@ -182,7 +226,10 @@ Reading state information... Reading extended state information... Initializing package states... Writing extended state information... -dpkg-deb: building package `sbuild-build-depends-bwa-dummy' in `/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi/resolver-xBK753/apt_archive/sbuild-build-depends-bwa-dummy.deb'. +Building tag database... +Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev +Filtered Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev +dpkg-deb: building package `sbuild-build-depends-bwa-dummy' in `/«BUILDDIR»/resolver-vEJtTq/apt_archive/sbuild-build-depends-bwa-dummy.deb'. OK Reading package lists... @@ -194,79 +241,148 @@ Reading package lists... Building dependency tree... Reading state information... aptitude is already the newest version. -0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. +0 upgraded, 0 newly installed, 0 to remove and 80 not upgraded. aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-bwa-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-bwa-dummy Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... +Building tag database... The following NEW packages will be installed: - debhelper{a} file{a} gettext{a} gettext-base{a} html2text{a} - intltool-debian{a} libcroco3{a} libffi5{a} libglib2.0-0{a} libmagic1{a} - libunistring0{a} libxml2{a} po-debconf{a} sbuild-build-depends-bwa-dummy + bsdmainutils{a} debhelper{a} file{a} gettext{a} gettext-base{a} + groff-base{a} intltool-debian{a} libasprintf0c2{a} libcroco3{a} + libffi6{a} libglib2.0-0{a} libmagic1{a} libpipeline1{a} libunistring0{a} + libxml2{a} man-db{a} po-debconf{a} sbuild-build-depends-bwa-dummy zlib1g-dev{a} -0 packages upgraded, 15 newly installed, 0 to remove and 2 not upgraded. -Need to get 0 B/6942 kB of archives. After unpacking 18.6 MB will be used. +The following packages will be upgraded: + zlib1g +1 packages upgraded, 19 newly installed, 0 to remove and 79 not upgraded. +Need to get 9083 kB/9084 kB of archives. After unpacking 26.0 MB will be used. Writing extended state information... +Get: 1 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g kfreebsd-amd64 1:1.2.8.dfsg-2+b1 [88.8 kB] +Get: 2 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.4.0-1 [27.9 kB] +Get: 3 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.22.3-1 [1077 kB] +Get: 4 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-amd64 9.0.6 [183 kB] +Get: 5 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.7.0.2-5 [995 kB] +Get: 6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.19.3-2 [31.3 kB] +Get: 7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 1:5.22+15-1 [249 kB] +Get: 8 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.9.2+dfsg1-1+b1 [905 kB] +Get: 9 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 kfreebsd-amd64 3.1-2+b2 [19.5 kB] +Get: 10 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.42.1-1 [2397 kB] +Get: 11 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.8-3+b1 [135 kB] +Get: 12 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5.2+b1 [287 kB] +Get: 13 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 1:5.22+15-1 [60.2 kB] +Get: 14 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.19.3-2 [121 kB] +Get: 15 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.19.3-2 [1236 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+nmu3 [220 kB] +Get: 18 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20150101 [813 kB] +Get: 19 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.8.dfsg-2+b1 [206 kB] +Fetched 9083 kB in 0s (23.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed -Selecting previously unselected package libffi5. -(Reading database ... 12474 files and directories currently installed.) -Unpacking libffi5 (from .../libffi5_3.0.10-3_kfreebsd-amd64.deb) ... -Selecting previously unselected package libglib2.0-0. -Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_kfreebsd-amd64.deb) ... -Selecting previously unselected package libxml2. -Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_kfreebsd-amd64.deb) ... -Selecting previously unselected package libcroco3. -Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-amd64.deb) ... -Selecting previously unselected package libunistring0. -Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ... -Selecting previously unselected package libmagic1. -Unpacking libmagic1 (from .../libmagic1_5.09-2_kfreebsd-amd64.deb) ... +(Reading database ... 11758 files and directories currently installed.) +Preparing to unpack .../zlib1g_1%3a1.2.8.dfsg-2+b1_kfreebsd-amd64.deb ... +Unpacking zlib1g:kfreebsd-amd64 (1:1.2.8.dfsg-2+b1) over (1:1.2.8.dfsg-2) ... +Setting up zlib1g:kfreebsd-amd64 (1:1.2.8.dfsg-2+b1) ... +Processing triggers for libc-bin (2.19-12) ... +Selecting previously unselected package libpipeline1:kfreebsd-amd64. +(Reading database ... 11759 files and directories currently installed.) +Preparing to unpack .../libpipeline1_1.4.0-1_kfreebsd-amd64.deb ... +Unpacking libpipeline1:kfreebsd-amd64 (1.4.0-1) ... +Selecting previously unselected package groff-base. +Preparing to unpack .../groff-base_1.22.3-1_kfreebsd-amd64.deb ... +Unpacking groff-base (1.22.3-1) ... +Selecting previously unselected package bsdmainutils. +Preparing to unpack .../bsdmainutils_9.0.6_kfreebsd-amd64.deb ... +Unpacking bsdmainutils (9.0.6) ... +Selecting previously unselected package man-db. +Preparing to unpack .../man-db_2.7.0.2-5_kfreebsd-amd64.deb ... +Unpacking man-db (2.7.0.2-5) ... +Selecting previously unselected package libasprintf0c2:kfreebsd-amd64. +Preparing to unpack .../libasprintf0c2_0.19.3-2_kfreebsd-amd64.deb ... +Unpacking libasprintf0c2:kfreebsd-amd64 (0.19.3-2) ... +Selecting previously unselected package libmagic1:kfreebsd-amd64. +Preparing to unpack .../libmagic1_1%3a5.22+15-1_kfreebsd-amd64.deb ... +Unpacking libmagic1:kfreebsd-amd64 (1:5.22+15-1) ... +Selecting previously unselected package libxml2:kfreebsd-amd64. +Preparing to unpack .../libxml2_2.9.2+dfsg1-1+b1_kfreebsd-amd64.deb ... +Unpacking libxml2:kfreebsd-amd64 (2.9.2+dfsg1-1+b1) ... +Selecting previously unselected package libffi6:kfreebsd-amd64. +Preparing to unpack .../libffi6_3.1-2+b2_kfreebsd-amd64.deb ... +Unpacking libffi6:kfreebsd-amd64 (3.1-2+b2) ... +Selecting previously unselected package libglib2.0-0:kfreebsd-amd64. +Preparing to unpack .../libglib2.0-0_2.42.1-1_kfreebsd-amd64.deb ... +Unpacking libglib2.0-0:kfreebsd-amd64 (2.42.1-1) ... +Selecting previously unselected package libcroco3:kfreebsd-amd64. +Preparing to unpack .../libcroco3_0.6.8-3+b1_kfreebsd-amd64.deb ... +Unpacking libcroco3:kfreebsd-amd64 (0.6.8-3+b1) ... +Selecting previously unselected package libunistring0:kfreebsd-amd64. +Preparing to unpack .../libunistring0_0.9.3-5.2+b1_kfreebsd-amd64.deb ... +Unpacking libunistring0:kfreebsd-amd64 (0.9.3-5.2+b1) ... Selecting previously unselected package file. -Unpacking file (from .../file_5.09-2_kfreebsd-amd64.deb) ... +Preparing to unpack .../file_1%3a5.22+15-1_kfreebsd-amd64.deb ... +Unpacking file (1:5.22+15-1) ... Selecting previously unselected package gettext-base. -Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_kfreebsd-amd64.deb) ... -Selecting previously unselected package html2text. -Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ... +Preparing to unpack .../gettext-base_0.19.3-2_kfreebsd-amd64.deb ... +Unpacking gettext-base (0.19.3-2) ... Selecting previously unselected package gettext. -Unpacking gettext (from .../gettext_0.18.1.1-5_kfreebsd-amd64.deb) ... +Preparing to unpack .../gettext_0.19.3-2_kfreebsd-amd64.deb ... +Unpacking gettext (0.19.3-2) ... Selecting previously unselected package intltool-debian. -Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... +Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... +Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. -Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... +Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ... +Unpacking po-debconf (1.0.16+nmu3) ... Selecting previously unselected package debhelper. -Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ... -Selecting previously unselected package zlib1g-dev. -Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-amd64.deb) ... +Preparing to unpack .../debhelper_9.20150101_all.deb ... +Unpacking debhelper (9.20150101) ... +Selecting previously unselected package zlib1g-dev:kfreebsd-amd64. +Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_kfreebsd-amd64.deb ... +Unpacking zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2+b1) ... Selecting previously unselected package sbuild-build-depends-bwa-dummy. -Unpacking sbuild-build-depends-bwa-dummy (from .../sbuild-build-depends-bwa-dummy.deb) ... -Processing triggers for man-db ... -Setting up libffi5 (3.0.10-3) ... -Setting up libglib2.0-0 (2.30.2-4) ... +Preparing to unpack .../sbuild-build-depends-bwa-dummy.deb ... +Unpacking sbuild-build-depends-bwa-dummy (0.invalid.0) ... +Setting up libpipeline1:kfreebsd-amd64 (1.4.0-1) ... +Setting up groff-base (1.22.3-1) ... +Setting up bsdmainutils (9.0.6) ... +update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode +update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode +Setting up man-db (2.7.0.2-5) ... +Not building database; man-db/auto-update is not 'true'. +Setting up libasprintf0c2:kfreebsd-amd64 (0.19.3-2) ... +Setting up libmagic1:kfreebsd-amd64 (1:5.22+15-1) ... +Setting up libxml2:kfreebsd-amd64 (2.9.2+dfsg1-1+b1) ... +Setting up libffi6:kfreebsd-amd64 (3.1-2+b2) ... +Setting up libglib2.0-0:kfreebsd-amd64 (2.42.1-1) ... 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 libmagic1 (5.09-2) ... -Setting up file (5.09-2) ... -Setting up gettext-base (0.18.1.1-5) ... -Setting up html2text (1.3.2a-15) ... -Setting up gettext (0.18.1.1-5) ... +Setting up libcroco3:kfreebsd-amd64 (0.6.8-3+b1) ... +Setting up libunistring0:kfreebsd-amd64 (0.9.3-5.2+b1) ... +Setting up file (1:5.22+15-1) ... +Setting up gettext-base (0.19.3-2) ... +Setting up gettext (0.19.3-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... -Setting up po-debconf (1.0.16+nmu1) ... -Setting up debhelper (8.9.11) ... -Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ... +Setting up po-debconf (1.0.16+nmu3) ... +Setting up debhelper (9.20150101) ... +Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2+b1) ... Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ... +Processing triggers for libc-bin (2.19-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... -Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64) -Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 kfreebsd-kernel-headers_0.60 libc0.1-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 -Package versions: adduser_3.113 apt_0.8.15.9 aptitude_0.6.4-1.2 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakero [...] +Building tag database... + +┌──────────────────────────────────────────────────────────────────────────────┐ +│ Build environment │ +└──────────────────────────────────────────────────────────────────────────────┘ + +Kernel: GNU/kFreeBSD 9.0-2-amd64 kfreebsd-amd64 (x86_64) +Toolchain package versions: binutils_2.24.90.20141014-1 dpkg-dev_1.17.20 g++-4.9_4.9.1-18 gcc-4.9_4.9.1-18 kfreebsd-kernel-headers_10.1~5 libc0.1-dev_2.19-12 libstdc++-4.9-dev_4.9.1-18 libstdc++6_4.9.1-18 +Package versions: apt_1.0.9.3 aptitude_0.6.11-1+b1 aptitude-common_0.6.11-1 base-files_7.8 base-passwd_3.5.36 bash_4.3-11 binutils_2.24.90.20141014-1 bsdmainutils_9.0.6 bsdutils_1:2.25.1-5 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-5 cpp-4.9_4.9.1-18 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-2 debhelper_9.20150101 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.20 dpkg-dev_1.17.20 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fa [...] ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ @@ -276,337 +392,171 @@ Package versions: adduser_3.113 apt_0.8.15.9 aptitude_0.6.4-1.2 base-files_6.5 b Unpack source ───────────── -gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error -gpgv: Signature made Tue Nov 22 02:41:12 2011 UTC using RSA key ID 2295D502 +gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error +gpgv: Signature made Tue Jan 27 07:49:47 2015 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found -dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-2.dsc -dpkg-source: info: extracting bwa in bwa-0.6.0 -dpkg-source: info: unpacking bwa_0.6.0-2.tar.gz +dpkg-source: warning: failed to verify signature on ./bwa_0.7.12-1.dsc +dpkg-source: info: extracting bwa in bwa-0.7.12 +dpkg-source: info: unpacking bwa_0.7.12.orig.tar.bz2 +dpkg-source: info: unpacking bwa_0.7.12-1.debian.tar.xz Check disc space ──────────────── +Sufficient free space for build + +User Environment +──────────────── + +DEB_BUILD_OPTIONS=parallel=2 +HOME=/sbuild-nonexistent +LOGNAME=buildd +PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games +SCHROOT_ALIAS_NAME=experimental-kfreebsd-amd64-sbuild +SCHROOT_CHROOT_NAME=sid-experimental-ka-sbuild +SCHROOT_COMMAND=env +SCHROOT_GID=1009 +SCHROOT_GROUP=buildd +SCHROOT_SESSION_ID=sid-experimental-ka-sbuild-1422548873-47431 +SCHROOT_UID=2952 +SCHROOT_USER=buildd +SHELL=/bin/sh +USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package bwa -dpkg-buildpackage: source version 0.6.0-2 - dpkg-source --before-build bwa-0.6.0 +dpkg-buildpackage: source version 0.7.12-1 +dpkg-buildpackage: source distribution experimental + dpkg-source --before-build bwa-0.7.12 dpkg-buildpackage: host architecture kfreebsd-amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean -make[1]: Entering directory `/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi/bwa-0.6.0' +make[1]: Entering directory '/«PKGBUILDDIR»' rm -f gmon.out *.o a.out bwa *~ *.a -make[1]: Leaving directory `/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi/bwa-0.6.0' +make[1]: Leaving directory '/«PKGBUILDDIR»' dh_clean - debian/rules build -dh build - dh_testdir - dh_auto_configure + debian/rules build-arch +dh build-arch + dh_testdir -a + dh_auto_configure -a debian/rules override_dh_auto_build -make[1]: Entering directory `/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi/bwa-0.6.0' -dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro" DFLAGS="-DHAVE_PTHREAD -D_NO_SSE2" -make[2]: Entering directory `/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi/bwa-0.6.0' -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 QSufSort.c -o QSufSort.o -QSufSort.c: In function 'QSufSortSuffixSort': -QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwt_gen.c -o bwt_gen.o +make[1]: Entering directory '/«PKGBUILDDIR»' +dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro" DFLAGS="-DHAVE_PTHREAD -D_NO_SSE2" +make[2]: Entering directory '/«PKGBUILDDIR»' +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 utils.c -o utils.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 kthread.c -o kthread.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 kstring.c -o kstring.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 ksw.c -o ksw.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwt.c -o bwt.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bntseq.c -o bntseq.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwa.c -o bwa.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwamem.c -o bwamem.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwamem_pair.c -o bwamem_pair.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwamem_extra.c -o bwamem_extra.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 malloc_wrap.c -o malloc_wrap.o +ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 QSufSort.c -o QSufSort.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwt_gen.c -o bwt_gen.o bwt_gen.c: In function 'BWTIncBuildRelativeRank': -bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable] +bwt_gen.c:878:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable] + bgint_t oldInverseSa0RelativeRank = 0; + ^ bwt_gen.c: In function 'BWTIncMergeBwt': -bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable] -bwt_gen.c: In function 'BWTIncConstructFromPacked': -bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 utils.c -o utils.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwt.c -o bwt.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtio.c -o bwtio.o -bwtio.c: In function 'bwt_restore_bwt': -bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtio.c: In function 'bwt_restore_sa': -bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtaln.c -o bwtaln.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtgap.c -o bwtgap.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 is.c -o is.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bntseq.c -o bntseq.o -bntseq.c: In function 'bns_restore_core': -bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] -bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] -bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] -bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] -bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtmisc.c -o bwtmisc.o -bwtmisc.c: In function 'bwa_pac2cspac_core': -bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtmisc.c: In function 'bwt_pac2bwt': -bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwtmisc.c: In function 'bwa_seq_len': -bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtindex.c -o bwtindex.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 ksw.c -o ksw.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 stdaln.c -o stdaln.o -stdaln.c: In function 'aln_local_core': -stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable] -stdaln.c: In function 'aln_extend_core': -stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 simple_dp.c -o simple_dp.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwaseqio.c -o bwaseqio.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwase.c -o bwase.o -bwase.c: In function 'bwa_aln2seq_core': -bwase.c:74:15: warning: variable 'k' set but not used [-Wunused-but-set-variable] -bwase.c: In function 'bwa_print_sam1': -bwase.c:447:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable] -bwase.c: In function 'bwa_sai2sam_se_core': -bwase.c:603:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwase.c:619:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwase.c:624:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwase.c: In function 'bwa_refine_gapped': -bwase.c:310:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwase.c:316:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwape.c -o bwape.o -bwape.c: In function 'bwa_sai2sam_pe_core': -bwape.c:683:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwape.c:686:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwape.c:697:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwape.c: In function 'bwa_paired_sw': -bwape.c:527:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwape.c: In function 'bwa_cal_pac_pos_pe': -bwape.c:312:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -bwape.c:316:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 kstring.c -o kstring.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 cs2nt.c -o cs2nt.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_core.c -o bwtsw2_core.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_main.c -o bwtsw2_main.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_aux.c -o bwtsw2_aux.o -bwtsw2_aux.c: In function 'gen_cigar': -bwtsw2_aux.c:186:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] -bwtsw2_aux.c: In function 'bsw2_aln': -bwtsw2_aux.c:734:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwt_lite.c -o bwt_lite.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_chain.c -o bwtsw2_chain.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bamlite.c -o bamlite.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 fastmap.c -o fastmap.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_pair.c -o bwtsw2_pair.o -gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 main.c -o main.o -gcc -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o fastmap.o bwtsw2_pair.o main.o -o bwa -lm -lz -lpthread -make[2]: Leaving directory `/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi/bwa-0.6.0' -make[1]: Leaving directory `/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi/bwa-0.6.0' - dh_auto_test - fakeroot debian/rules binary-arch -dh binary-arch - dh_testroot -a - dh_prep -a - dh_installdirs -a - dh_auto_install -a - dh_install -a - dh_installdocs -a - dh_installchangelogs -a - dh_installexamples -a - dh_installman -a - dh_installcatalogs -a - dh_installcron -a - dh_installdebconf -a - dh_installemacsen -a - dh_installifupdown -a - dh_installinfo -a - dh_installinit -a - dh_installmenu -a - dh_installmime -a - dh_installmodules -a - dh_installlogcheck -a - dh_installlogrotate -a - dh_installpam -a - dh_installppp -a - dh_installudev -a - dh_installwm -a - dh_installxfonts -a - dh_installgsettings -a - dh_bugfiles -a - dh_ucf -a - dh_lintian -a - dh_gconf -a - dh_icons -a - dh_perl -a - dh_usrlocal -a - dh_link -a - dh_compress -a - dh_fixperms -a - dh_strip -a - dh_makeshlibs -a - dh_shlibdeps -a - dh_installdeb -a - dh_gencontrol -a -dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends} - dh_md5sums -a - dh_builddeb -a -dpkg-deb: building package `bwa' in `../bwa_0.6.0-2_kfreebsd-amd64.deb'. - dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <[email protected]> >../bwa_0.6.0-2_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 bwa-0.6.0 -dpkg-buildpackage: binary only upload (no source included) +bwt_gen.c:952:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable] + unsigned int bitsInWordMinusBitPerChar; + ^ +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwashm.c -o bwashm.o +bwashm.c: In function 'bwa_shm_stage': +bwashm.c:29:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result] + ftruncate(shmid, BWA_CTL_SIZE); + ^ +bwashm.c:66:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result] + ftruncate(shmid, idx->l_mem); + ^ +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwase.c -o bwase.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwaseqio.c -o bwaseqio.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtgap.c -o bwtgap.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtaln.c -o bwtaln.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bamlite.c -o bamlite.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 is.c -o is.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtindex.c -o bwtindex.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwape.c -o bwape.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 kopen.c -o kopen.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 pemerge.c -o pemerge.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_core.c -o bwtsw2_core.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_main.c -o bwtsw2_main.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_aux.c -o bwtsw2_aux.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwt_lite.c -o bwt_lite.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_chain.c -o bwtsw2_chain.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 fastmap.c -o fastmap.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 bwtsw2_pair.c -o bwtsw2_pair.o +gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 main.c -o main.o +gcc -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread +bwashm.o: In function `bwa_shm_test': +/«PKGBUILDDIR»/bwashm.c:130: undefined reference to `shm_open' +bwashm.o: In function `bwa_shm_stage': +/«PKGBUILDDIR»/bwashm.c:24: undefined reference to `shm_open' +/«PKGBUILDDIR»/bwashm.c:56: undefined reference to `shm_open' +/«PKGBUILDDIR»/bwashm.c:57: undefined reference to `shm_unlink' +/«PKGBUILDDIR»/bwashm.c:25: undefined reference to `shm_open' +bwashm.o: In function `bwa_idx_load_from_shm': +/«PKGBUILDDIR»/bwashm.c:100: undefined reference to `shm_open' +/«PKGBUILDDIR»/bwashm.c:112: undefined reference to `shm_open' +bwashm.o: In function `bwa_shm_list': +/«PKGBUILDDIR»/bwashm.c:145: undefined reference to `shm_open' +bwashm.o: In function `bwa_shm_destroy': +/«PKGBUILDDIR»/bwashm.c:164: undefined reference to `shm_open' +/«PKGBUILDDIR»/bwashm.c:171: undefined reference to `shm_unlink' +/«PKGBUILDDIR»/bwashm.c:175: undefined reference to `shm_unlink' +collect2: error: ld returned 1 exit status +make[2]: *** [bwa] Error 1 +Makefile:29: recipe for target 'bwa' failed +make[2]: Leaving directory '/«PKGBUILDDIR»' +dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro DFLAGS=-DHAVE_PTHREAD -D_NO_SSE2 returned exit code 2 +make[1]: *** [override_dh_auto_build] Error 2 +debian/rules:15: recipe for target 'override_dh_auto_build' failed +make[1]: Leaving directory '/«PKGBUILDDIR»' +make: *** [build-arch] Error 2 +debian/rules:4: recipe for target 'build-arch' failed +dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── -Build finished at 20111122-0321 - -bwa_0.6.0-2_kfreebsd-amd64.changes: -Format: 1.8 -Date: Tue, 22 Nov 2011 11:32:11 +0900 -Source: bwa -Binary: bwa -Architecture: kfreebsd-amd64 -Version: 0.6.0-2 -Distribution: experimental -Urgency: low -Maintainer: kfreebsd-amd64 Build Daemon (fano) <[email protected]> -Changed-By: Charles Plessy <[email protected]> -Description: - bwa - Burrows-Wheeler Aligner -Closes: 648803 -Changes: - bwa (0.6.0-2) experimental; urgency=low - . - [9410de3] Disable SSE2 everywhere except on amd64 (Closes: #648803). - [fb4c559] Reimplementation of Standard SW for when SSE2 is unavailable. - cherry picked from upstream commit 182cb2e. - This commit modifies upstream sources. - [9c93ccd] Use native format to bypass mandatory patch system. -Checksums-Sha1: - 40141db7501b702852a59f4f9a0adb83fee5ffbd 149368 bwa_0.6.0-2_kfreebsd-amd64.deb -Checksums-Sha256: - f6d8f4839af2e03695fa844294b07be15239390edaa8f51eadcf6cb70ffc7a54 149368 bwa_0.6.0-2_kfreebsd-amd64.deb -Files: - 92ce3c3f917767eaab8bc69c00053314 149368 science optional bwa_0.6.0-2_kfreebsd-amd64.deb - -┌──────────────────────────────────────────────────────────────────────────────┐ -│ Package contents │ -└──────────────────────────────────────────────────────────────────────────────┘ +Build finished at 20150129-1629 +Finished +──────── -bwa_0.6.0-2_kfreebsd-amd64.deb -────────────────────────────── - - new debian package, version 2.0. - size 149368 bytes: control archive= 997 bytes. - 785 bytes, 17 lines control - 610 bytes, 10 lines md5sums - Package: bwa - Version: 0.6.0-2 - Architecture: kfreebsd-amd64 - Maintainer: Debian Med Packaging Team <[email protected]> - Installed-Size: 257 - Depends: libc0.1 (>= 2.7), zlib1g (>= 1:1.1.4) - Suggests: samtools - Section: science - Priority: optional - Homepage: http://bio-bwa.sourceforge.net/ - Description: Burrows-Wheeler Aligner - Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short - nucleotide sequences against a long reference sequence such as the human - genome. It implements two algorithms, bwa-short and BWA-SW. The former works - for query sequences shorter than 200 bp and the latter for longer sequences up - to around 100 kbp. Both algorithms do gapped alignment. They are usually more - accurate and faster on queries with low error rates. - -drwxr-xr-x root/root 0 2011-11-22 03:21 ./ -drwxr-xr-x root/root 0 2011-11-22 03:21 ./usr/ -drwxr-xr-x root/root 0 2011-11-22 03:21 ./usr/bin/ --rwxr-xr-x root/root 215656 2011-11-22 03:21 ./usr/bin/bwa -drwxr-xr-x root/root 0 2011-11-22 03:21 ./usr/share/ -drwxr-xr-x root/root 0 2011-11-22 03:21 ./usr/share/bwa/ --rwxr-xr-x root/root 3176 2011-11-22 01:55 ./usr/share/bwa/solid2fastq.pl --rwxr-xr-x root/root 616 2011-11-22 01:55 ./usr/share/bwa/qualfa2fq.pl --rwxr-xr-x root/root 730 2011-11-22 01:55 ./usr/share/bwa/xa2multi.pl -drwxr-xr-x root/root 0 2011-11-22 03:21 ./usr/share/doc/ -drwxr-xr-x root/root 0 2011-11-22 03:21 ./usr/share/doc/bwa/ --rw-r--r-- root/root 634 2011-11-22 01:55 ./usr/share/doc/bwa/README --rw-r--r-- root/root 2785 2011-11-22 01:55 ./usr/share/doc/bwa/copyright --rw-r--r-- root/root 17912 2011-11-22 01:55 ./usr/share/doc/bwa/changelog.gz --rw-r--r-- root/root 6680 2011-11-22 01:55 ./usr/share/doc/bwa/NEWS.gz --rw-r--r-- root/root 1471 2011-11-22 02:32 ./usr/share/doc/bwa/changelog.Debian.gz -drwxr-xr-x root/root 0 2011-11-22 03:21 ./usr/share/man/ -drwxr-xr-x root/root 0 2011-11-22 03:21 ./usr/share/man/man1/ --rw-r--r-- root/root 7745 2011-11-22 03:21 ./usr/share/man/man1/bwa.1.gz - +E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ -│ Finished │ +│ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ -Built successfully -──────────────────────────────────────────────────────────────────────────────── - -┌──────────────────────────────────────────────────────────────────────────────┐ -│ Post Build │ -└──────────────────────────────────────────────────────────────────────────────┘ - -Purging /var/lib/schroot/mount/experimental-ka-sbuild-1321931992-81990/build/buildd-bwa_0.6.0-2-kfreebsd-amd64-2lhsBi -Reading package lists... -Building dependency tree... -Reading state information... -0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. -Reading package lists... -Building dependency tree... -Reading state information... -The following packages will be REMOVED: - debhelper* file* gettext* gettext-base* html2text* intltool-debian* - libcroco3* libffi5* libglib2.0-0* libmagic1* libunistring0* libxml2* - po-debconf* sbuild-build-depends-bwa-dummy* sbuild-build-depends-core-dummy* - zlib1g-dev* -0 upgraded, 0 newly installed, 16 to remove and 2 not upgraded. -After this operation, 18.6 MB disk space will be freed. -(Reading database ... 13300 files and directories currently installed.) -Removing sbuild-build-depends-bwa-dummy ... -Removing debhelper ... -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 libglib2.0-0 ... -Purging configuration files for libglib2.0-0 ... -Removing libffi5 ... -Purging configuration files for libffi5 ... -Removing libmagic1 ... -Purging configuration files for libmagic1 ... -Removing libunistring0 ... -Purging configuration files for libunistring0 ... -Removing libxml2 ... -Purging configuration files for libxml2 ... -Removing sbuild-build-depends-core-dummy ... -Removing zlib1g-dev ... -Processing triggers for man-db ... +Purging /«BUILDDIR» +Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ -Architecture: kfreebsd-amd64 -Build-Space: 3176 -Build-Time: 25 +Build Architecture: kfreebsd-amd64 +Build-Space: 3798 +Build-Time: 27 Distribution: experimental -Install-Time: 50 -Job: bwa_0.6.0-2 +Fail-Stage: build +Host Architecture: kfreebsd-amd64 +Install-Time: 37 +Job: bwa_0.7.12-1 +Machine Architecture: kfreebsd-amd64 Package: bwa -Package-Time: 96 -Source-Version: 0.6.0-2 -Space: 3176 -Status: successful -Version: 0.6.0-2 +Package-Time: 108 +Source-Version: 0.7.12-1 +Space: 3798 +Status: attempted +Version: 0.7.12-1 ──────────────────────────────────────────────────────────────────────────────── -Finished at 20111122-0321 -Build needed 00:01:36, 3176k disc space -Signature with key 'D33FE1D8' requested: +Finished at 20150129-1629 +Build needed 00:01:48, 3798k disc space -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bwa.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
