[med-svn] [SCM] bwa branch, meta, updated. 1d4815cde904089c4f8e680eb3aa98d1240f088d
Charles Plessy
plessy at debian.org
Sun Nov 13 10:29:52 UTC 2011
The following commit has been merged in the meta branch:
commit f08ad040a0c4a4df547aeae6f1fc6cd24404b44f
Author: Charles Plessy <plessy at debian.org>
Date: Sun Nov 13 19:25:34 2011 +0900
Buid logs for 0.5.9-1.
diff --git a/alpha.log b/alpha.log
index 593c3d9..b38eb48 100644
--- a/alpha.log
+++ b/alpha.log
@@ -1,212 +1,61 @@
-From buildd at goetz.debian.org Wed Oct 27 12:41:43 2010
-Return-path: <buildd at goetz.debian.org>
+From buildd at goedel.debian.org Tue Feb 08 11:19:41 2011
+Return-path: <buildd at goedel.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
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 4.69) (envelope-from <buildd at goetz.debian.org>)
- id 1PB5K2-00052p-Rr
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:41:43 +0000
-Received: from goetz.debian.org ([193.62.202.26])
+ (Exim 4.69) (envelope-from <buildd at goedel.debian.org>)
+ id 1Pmlbh-0006f7-79
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 11:19:41 +0000
+Received: from goedel.cst.com ([213.188.99.214] helo=goedel.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=goetz.debian.org, EMAIL=hostmaster at goetz.debian.org (verified)
+ CN=goedel.debian.org, EMAIL=hostmaster at goedel.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at goetz.debian.org>)
- id 1PB5K1-0004dm-Ja; Wed, 27 Oct 2010 12:41:41 +0000
-Received: from buildd by goetz.debian.org with local (Exim 4.69)
- (envelope-from <buildd at goetz.debian.org>)
- id 1PB5Jw-0007k4-9S; Wed, 27 Oct 2010 12:41:36 +0000
-From: buildd on goetz <buildd at goetz.debian.org>
+ (Exim 4.69) (envelope-from <buildd at goedel.debian.org>)
+ id 1Pmlbg-00059R-3X; Tue, 08 Feb 2011 11:19:40 +0000
+Received: from buildd by goedel.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at goedel.debian.org>)
+ id 1Pmlbd-0004cA-Dj; Tue, 08 Feb 2011 11:19:37 +0000
+From: buildd at goedel.debian.org
To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on alpha (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on alpha (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PB5Jw-0007k4-9S at goetz.debian.org>
-Date: Wed, 27 Oct 2010 12:41:36 +0000
+Message-Id: <E1Pmlbd-0004cA-Dj at goedel.debian.org>
+Date: Tue, 08 Feb 2011 11:19:37 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on goetz.debian.org
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on goedel.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (alpha) 27 Oct 2010 12:38 ║
+║ bwa 0.5.9-1 (alpha) 08 Feb 2011 11:17 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: alpha
-Chroot Build Dir: /var/lib/schroot/mount/sid-alpha-sbuild-35e99b14-4f1f-47f6-9875-7e8ad7b7d7b2/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR
-Start Time: 20101027-1238
-Get:1 http://ftp.uk.debian.org sid Release.gpg [835B]
-Ign http://ftp.uk.debian.org/debian/ sid/contrib Translation-en
-Ign http://ftp.uk.debian.org/debian/ sid/main Translation-en
-Get:2 http://ftp.uk.debian.org sid Release [104kB]
-Get:3 http://incoming.debian.org sid Release.gpg [835B]
+Chroot Build Dir: /var/lib/schroot/mount/sid-alpha-sbuild-33a5461a-cb7a-41b3-85a6-02c69a43ad38/build/buildd-bwa_0.5.9-1-alpha-RA1JNc
+Start Time: 20110208-1117
+Hit http://ftp.de.debian.org sid Release.gpg
+Ign http://ftp.de.debian.org/debian/ sid/contrib Translation-en
+Ign http://ftp.de.debian.org/debian/ sid/main Translation-en
+Hit http://ftp.de.debian.org sid Release
+Hit http://ftp.de.debian.org sid/main alpha Packages/DiffIndex
+Hit http://incoming.debian.org sid Release.gpg
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:4 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038B]
-Get:5 http://incoming.debian.org Release.gpg [835B]
+Hit http://incoming.debian.org Release.gpg
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:6 http://incoming.debian.org sid Release [104kB]
-Get:7 http://ftp.uk.debian.org sid/contrib Sources/DiffIndex [2023B]
-Get:8 http://ftp.uk.debian.org sid/main alpha Packages/DiffIndex [2038B]
-Get:9 http://ftp.uk.debian.org sid/contrib alpha Packages/DiffIndex [2023B]
-Get:10 http://incoming.debian.org Release [1604B]
-Get:11 http://ftp.uk.debian.org sid/main Sources [4008kB]
-Get:12 http://incoming.debian.org sid/main Sources/DiffIndex [2038B]
-Get:13 http://incoming.debian.org sid/contrib Sources/DiffIndex [2023B]
-Get:14 http://incoming.debian.org sid/main alpha Packages/DiffIndex [2038B]
-Get:15 http://incoming.debian.org sid/contrib alpha Packages/DiffIndex [2023B]
-Get:16 http://incoming.debian.org Sources [23.4kB]
-Get:17 http://incoming.debian.org Packages [85.4kB]
-Get:18 http://incoming.debian.org sid/main Sources [4008kB]
-Get:19 http://ftp.uk.debian.org sid/contrib 2010-09-07-0211.31.pdiff [349B]
-Get:20 http://ftp.uk.debian.org sid/main alpha Packages [6648kB]
-Get:21 http://ftp.uk.debian.org sid/contrib 2010-09-07-0211.31.pdiff [349B]
-Get:22 http://ftp.uk.debian.org sid/contrib 2010-09-07-0211.31.pdiff [349B]
-Get:23 http://ftp.uk.debian.org sid/contrib alpha 2010-09-11-1410.37.pdiff [249B]
-Get:24 http://ftp.uk.debian.org sid/contrib alpha 2010-09-11-1410.37.pdiff [249B]
-Get:25 http://ftp.uk.debian.org sid/contrib alpha 2010-09-11-1410.37.pdiff [249B]
-Get:26 http://ftp.uk.debian.org sid/contrib 2010-09-07-0813.20.pdiff [274B]
-Get:27 http://ftp.uk.debian.org sid/contrib 2010-09-07-0813.20.pdiff [274B]
-Get:28 http://ftp.uk.debian.org sid/contrib 2010-09-07-0813.20.pdiff [274B]
-Get:29 http://ftp.uk.debian.org sid/contrib alpha 2010-09-19-0208.49.pdiff [264B]
-Get:30 http://ftp.uk.debian.org sid/contrib alpha 2010-09-19-0208.49.pdiff [264B]
-Get:31 http://ftp.uk.debian.org sid/contrib alpha 2010-09-19-0208.49.pdiff [264B]
-Get:32 http://ftp.uk.debian.org sid/contrib 2010-09-08-1409.42.pdiff [31B]
-Get:33 http://ftp.uk.debian.org sid/contrib 2010-09-08-1409.42.pdiff [31B]
-Get:34 http://ftp.uk.debian.org sid/contrib 2010-09-08-1409.42.pdiff [31B]
-Get:35 http://ftp.uk.debian.org sid/contrib alpha 2010-09-21-0811.00.pdiff [534B]
-Get:36 http://ftp.uk.debian.org sid/contrib alpha 2010-09-21-0811.00.pdiff [534B]
-Get:37 http://ftp.uk.debian.org sid/contrib alpha 2010-09-21-0811.00.pdiff [534B]
-Get:38 http://ftp.uk.debian.org sid/contrib 2010-09-09-2014.53.pdiff [29B]
-Get:39 http://ftp.uk.debian.org sid/contrib 2010-09-09-2014.53.pdiff [29B]
-Get:40 http://ftp.uk.debian.org sid/contrib 2010-09-09-2014.53.pdiff [29B]
-Get:41 http://ftp.uk.debian.org sid/contrib alpha 2010-09-21-1410.02.pdiff [221B]
-Get:42 http://ftp.uk.debian.org sid/contrib alpha 2010-09-21-1410.02.pdiff [221B]
-Get:43 http://ftp.uk.debian.org sid/contrib alpha 2010-09-21-1410.02.pdiff [221B]
-Get:44 http://ftp.uk.debian.org sid/contrib 2010-09-11-1410.37.pdiff [211B]
-Get:45 http://ftp.uk.debian.org sid/contrib 2010-09-11-1410.37.pdiff [211B]
-Get:46 http://ftp.uk.debian.org sid/contrib 2010-09-11-1410.37.pdiff [211B]
-Get:47 http://ftp.uk.debian.org sid/contrib alpha 2010-09-22-2010.38.pdiff [416B]
-Get:48 http://ftp.uk.debian.org sid/contrib alpha 2010-09-22-2010.38.pdiff [416B]
-Get:49 http://ftp.uk.debian.org sid/contrib alpha 2010-09-22-2010.38.pdiff [416B]
-Get:50 http://ftp.uk.debian.org sid/contrib 2010-09-17-2201.43.pdiff [435B]
-Get:51 http://ftp.uk.debian.org sid/contrib 2010-09-17-2201.43.pdiff [435B]
-Get:52 http://ftp.uk.debian.org sid/contrib 2010-09-17-2201.43.pdiff [435B]
-Get:53 http://ftp.uk.debian.org sid/contrib alpha 2010-09-26-2015.44.pdiff [29B]
-Get:54 http://ftp.uk.debian.org sid/contrib alpha 2010-09-26-2015.44.pdiff [29B]
-Get:55 http://ftp.uk.debian.org sid/contrib alpha 2010-09-26-2015.44.pdiff [29B]
-Get:56 http://ftp.uk.debian.org sid/contrib 2010-09-18-1438.18.pdiff [29B]
-Get:57 http://ftp.uk.debian.org sid/contrib 2010-09-18-1438.18.pdiff [29B]
-Get:58 http://ftp.uk.debian.org sid/contrib 2010-09-18-1438.18.pdiff [29B]
-Get:59 http://ftp.uk.debian.org sid/contrib alpha 2010-09-28-1416.16.pdiff [267B]
-Get:60 http://ftp.uk.debian.org sid/contrib alpha 2010-09-28-1416.16.pdiff [267B]
-Get:61 http://ftp.uk.debian.org sid/contrib alpha 2010-09-28-1416.16.pdiff [267B]
-Get:62 http://ftp.uk.debian.org sid/contrib 2010-09-19-0208.49.pdiff [401B]
-Get:63 http://ftp.uk.debian.org sid/contrib 2010-09-19-0208.49.pdiff [401B]
-Get:64 http://ftp.uk.debian.org sid/contrib 2010-09-19-0208.49.pdiff [401B]
-Get:65 http://ftp.uk.debian.org sid/contrib alpha 2010-10-01-0210.53.pdiff [614B]
-Get:66 http://ftp.uk.debian.org sid/contrib alpha 2010-10-01-0210.53.pdiff [614B]
-Get:67 http://ftp.uk.debian.org sid/contrib alpha 2010-10-01-0210.53.pdiff [614B]
-Get:68 http://ftp.uk.debian.org sid/contrib 2010-09-21-1410.02.pdiff [330B]
-Get:69 http://ftp.uk.debian.org sid/contrib 2010-09-21-1410.02.pdiff [330B]
-Get:70 http://ftp.uk.debian.org sid/contrib 2010-09-21-1410.02.pdiff [330B]
-Get:71 http://ftp.uk.debian.org sid/contrib alpha 2010-10-18-2025.39.pdiff [883B]
-Get:72 http://ftp.uk.debian.org sid/contrib alpha 2010-10-18-2025.39.pdiff [883B]
-Get:73 http://ftp.uk.debian.org sid/contrib alpha 2010-10-18-2025.39.pdiff [883B]
-Get:74 http://ftp.uk.debian.org sid/contrib 2010-09-22-1410.07.pdiff [720B]
-Get:75 http://ftp.uk.debian.org sid/contrib 2010-09-22-1410.07.pdiff [720B]
-Get:76 http://ftp.uk.debian.org sid/contrib 2010-09-22-1410.07.pdiff [720B]
-Get:77 http://ftp.uk.debian.org sid/contrib alpha 2010-10-19-1442.44.pdiff [31B]
-Get:78 http://incoming.debian.org sid/contrib 2010-09-07-0211.31.pdiff [349B]
-Get:79 http://incoming.debian.org sid/contrib 2010-09-07-0211.31.pdiff [349B]
-Get:80 http://incoming.debian.org sid/contrib 2010-09-07-0211.31.pdiff [349B]
-Get:81 http://incoming.debian.org sid/main alpha Packages [6648kB]
-Get:82 http://ftp.uk.debian.org sid/contrib alpha 2010-10-19-1442.44.pdiff [31B]
-Get:83 http://ftp.uk.debian.org sid/contrib alpha 2010-10-19-1442.44.pdiff [31B]
-Get:84 http://ftp.uk.debian.org sid/contrib 2010-09-28-0212.16.pdiff [29B]
-Get:85 http://ftp.uk.debian.org sid/contrib 2010-09-28-0212.16.pdiff [29B]
-Get:86 http://ftp.uk.debian.org sid/contrib 2010-09-28-0212.16.pdiff [29B]
-Get:87 http://ftp.uk.debian.org sid/contrib 2010-09-28-1416.16.pdiff [220B]
-Get:88 http://ftp.uk.debian.org sid/contrib 2010-09-28-1416.16.pdiff [220B]
-Get:89 http://ftp.uk.debian.org sid/contrib 2010-09-28-1416.16.pdiff [220B]
-Get:90 http://ftp.uk.debian.org sid/contrib 2010-10-18-2025.39.pdiff [622B]
-Get:91 http://ftp.uk.debian.org sid/contrib 2010-10-18-2025.39.pdiff [622B]
-Get:92 http://ftp.uk.debian.org sid/contrib 2010-10-18-2025.39.pdiff [622B]
-Get:93 http://ftp.uk.debian.org sid/contrib 2010-10-19-1442.44.pdiff [31B]
-Get:94 http://ftp.uk.debian.org sid/contrib 2010-10-19-1442.44.pdiff [31B]
-Get:95 http://ftp.uk.debian.org sid/contrib 2010-10-19-1442.44.pdiff [31B]
-Get:96 http://incoming.debian.org sid/contrib alpha 2010-09-11-1410.37.pdiff [249B]
-Get:97 http://incoming.debian.org sid/contrib alpha 2010-09-11-1410.37.pdiff [249B]
-Get:98 http://incoming.debian.org sid/contrib alpha 2010-09-11-1410.37.pdiff [249B]
-Get:99 http://incoming.debian.org sid/contrib 2010-09-07-0813.20.pdiff [274B]
-Get:100 http://incoming.debian.org sid/contrib 2010-09-07-0813.20.pdiff [274B]
-Get:101 http://incoming.debian.org sid/contrib alpha 2010-09-19-0208.49.pdiff [264B]
-Get:102 http://incoming.debian.org sid/contrib 2010-09-07-0813.20.pdiff [274B]
-Get:103 http://incoming.debian.org sid/contrib alpha 2010-09-19-0208.49.pdiff [264B]
-Get:104 http://incoming.debian.org sid/contrib alpha 2010-09-19-0208.49.pdiff [264B]
-Get:105 http://incoming.debian.org sid/contrib 2010-09-08-1409.42.pdiff [31B]
-Get:106 http://incoming.debian.org sid/contrib 2010-09-08-1409.42.pdiff [31B]
-Get:107 http://incoming.debian.org sid/contrib 2010-09-08-1409.42.pdiff [31B]
-Get:108 http://incoming.debian.org sid/contrib alpha 2010-09-21-0811.00.pdiff [534B]
-Get:109 http://incoming.debian.org sid/contrib alpha 2010-09-21-0811.00.pdiff [534B]
-Get:110 http://incoming.debian.org sid/contrib alpha 2010-09-21-0811.00.pdiff [534B]
-Get:111 http://incoming.debian.org sid/contrib 2010-09-09-2014.53.pdiff [29B]
-Get:112 http://incoming.debian.org sid/contrib 2010-09-09-2014.53.pdiff [29B]
-Get:113 http://incoming.debian.org sid/contrib 2010-09-09-2014.53.pdiff [29B]
-Get:114 http://incoming.debian.org sid/contrib alpha 2010-09-21-1410.02.pdiff [221B]
-Get:115 http://incoming.debian.org sid/contrib alpha 2010-09-21-1410.02.pdiff [221B]
-Get:116 http://incoming.debian.org sid/contrib alpha 2010-09-21-1410.02.pdiff [221B]
-Get:117 http://incoming.debian.org sid/contrib 2010-09-11-1410.37.pdiff [211B]
-Get:118 http://incoming.debian.org sid/contrib 2010-09-11-1410.37.pdiff [211B]
-Get:119 http://incoming.debian.org sid/contrib 2010-09-11-1410.37.pdiff [211B]
-Get:120 http://incoming.debian.org sid/contrib alpha 2010-09-22-2010.38.pdiff [416B]
-Get:121 http://incoming.debian.org sid/contrib alpha 2010-09-22-2010.38.pdiff [416B]
-Get:122 http://incoming.debian.org sid/contrib alpha 2010-09-22-2010.38.pdiff [416B]
-Get:123 http://incoming.debian.org sid/contrib 2010-09-17-2201.43.pdiff [435B]
-Get:124 http://incoming.debian.org sid/contrib 2010-09-17-2201.43.pdiff [435B]
-Get:125 http://incoming.debian.org sid/contrib 2010-09-17-2201.43.pdiff [435B]
-Get:126 http://incoming.debian.org sid/contrib alpha 2010-09-26-2015.44.pdiff [29B]
-Get:127 http://incoming.debian.org sid/contrib alpha 2010-09-26-2015.44.pdiff [29B]
-Get:128 http://incoming.debian.org sid/contrib alpha 2010-09-26-2015.44.pdiff [29B]
-Get:129 http://incoming.debian.org sid/contrib 2010-09-18-1438.18.pdiff [29B]
-Get:130 http://incoming.debian.org sid/contrib 2010-09-18-1438.18.pdiff [29B]
-Get:131 http://incoming.debian.org sid/contrib 2010-09-18-1438.18.pdiff [29B]
-Get:132 http://incoming.debian.org sid/contrib alpha 2010-09-28-1416.16.pdiff [267B]
-Get:133 http://incoming.debian.org sid/contrib alpha 2010-09-28-1416.16.pdiff [267B]
-Get:134 http://incoming.debian.org sid/contrib alpha 2010-09-28-1416.16.pdiff [267B]
-Get:135 http://incoming.debian.org sid/contrib 2010-09-19-0208.49.pdiff [401B]
-Get:136 http://incoming.debian.org sid/contrib 2010-09-19-0208.49.pdiff [401B]
-Get:137 http://incoming.debian.org sid/contrib 2010-09-19-0208.49.pdiff [401B]
-Get:138 http://incoming.debian.org sid/contrib alpha 2010-10-01-0210.53.pdiff [614B]
-Get:139 http://incoming.debian.org sid/contrib alpha 2010-10-01-0210.53.pdiff [614B]
-Get:140 http://incoming.debian.org sid/contrib alpha 2010-10-01-0210.53.pdiff [614B]
-Get:141 http://incoming.debian.org sid/contrib 2010-09-21-1410.02.pdiff [330B]
-Get:142 http://incoming.debian.org sid/contrib 2010-09-21-1410.02.pdiff [330B]
-Get:143 http://incoming.debian.org sid/contrib 2010-09-21-1410.02.pdiff [330B]
-Get:144 http://incoming.debian.org sid/contrib alpha 2010-10-18-2025.39.pdiff [883B]
-Get:145 http://incoming.debian.org sid/contrib alpha 2010-10-18-2025.39.pdiff [883B]
-Get:146 http://incoming.debian.org sid/contrib alpha 2010-10-18-2025.39.pdiff [883B]
-Get:147 http://incoming.debian.org sid/contrib 2010-09-22-1410.07.pdiff [720B]
-Get:148 http://incoming.debian.org sid/contrib 2010-09-22-1410.07.pdiff [720B]
-Get:149 http://incoming.debian.org sid/contrib 2010-09-22-1410.07.pdiff [720B]
-Get:150 http://incoming.debian.org sid/contrib alpha 2010-10-19-1442.44.pdiff [31B]
-Get:151 http://incoming.debian.org sid/contrib alpha 2010-10-19-1442.44.pdiff [31B]
-Get:152 http://incoming.debian.org sid/contrib alpha 2010-10-19-1442.44.pdiff [31B]
-Get:153 http://incoming.debian.org sid/contrib 2010-09-28-0212.16.pdiff [29B]
-Get:154 http://incoming.debian.org sid/contrib 2010-09-28-0212.16.pdiff [29B]
-Get:155 http://incoming.debian.org sid/contrib 2010-09-28-0212.16.pdiff [29B]
-Get:156 http://incoming.debian.org sid/contrib 2010-09-28-1416.16.pdiff [220B]
-Get:157 http://incoming.debian.org sid/contrib 2010-09-28-1416.16.pdiff [220B]
-Get:158 http://incoming.debian.org sid/contrib 2010-09-28-1416.16.pdiff [220B]
-Get:159 http://incoming.debian.org sid/contrib 2010-10-18-2025.39.pdiff [622B]
-Get:160 http://incoming.debian.org sid/contrib 2010-10-18-2025.39.pdiff [622B]
-Get:161 http://incoming.debian.org sid/contrib 2010-10-18-2025.39.pdiff [622B]
-Get:162 http://incoming.debian.org sid/contrib 2010-10-19-1442.44.pdiff [31B]
-Get:163 http://incoming.debian.org sid/contrib 2010-10-19-1442.44.pdiff [31B]
-Get:164 http://incoming.debian.org sid/contrib 2010-10-19-1442.44.pdiff [31B]
-Fetched 21.7MB in 48s (448kB/s)
+Hit http://ftp.de.debian.org sid/contrib alpha Packages/DiffIndex
+Hit http://incoming.debian.org sid Release
+Hit http://incoming.debian.org Release
+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 alpha Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib alpha Packages/DiffIndex
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -225,20 +74,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 5s (20.9kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 0s (171 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -246,114 +95,36 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
-debhelper: missing
-Using default version 8.0.0
+debhelper: already installed (8.0.0 >= 8 is satisfied)
zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies: cdbs debhelper zlib1g-dev
+Installing positive dependencies: cdbs zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
- po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ devscripts doc-base
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
- libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 51 not upgraded.
-Need to get 10.9MB of archives.
-After this operation, 31.6MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ sid/main bsdmainutils alpha 8.0.13 [212kB]
-Get:2 http://ftp.uk.debian.org/debian/ sid/main groff-base alpha 1.20.1-10 [1210kB]
-Get:3 http://ftp.uk.debian.org/debian/ sid/main man-db alpha 2.5.7-6 [1624kB]
-Get:4 http://ftp.uk.debian.org/debian/ sid/main libmagic1 alpha 5.04-5 [243kB]
-Get:5 http://ftp.uk.debian.org/debian/ sid/main file alpha 5.04-5 [50.2kB]
-Get:6 http://ftp.uk.debian.org/debian/ sid/main gettext-base alpha 0.18.1.1-3 [160kB]
-Get:7 http://ftp.uk.debian.org/debian/ sid/main libpcre3 alpha 8.02-1.1 [250kB]
-Get:8 http://ftp.uk.debian.org/debian/ sid/main libxml2 alpha 2.7.7.dfsg-4 [900kB]
-Get:9 http://ftp.uk.debian.org/debian/ sid/main html2text alpha 1.3.2a-15 [111kB]
-Get:10 http://ftp.uk.debian.org/debian/ sid/main libglib2.0-0 alpha 2.24.2-1 [1168kB]
-Get:11 http://ftp.uk.debian.org/debian/ sid/main libcroco3 alpha 0.6.2-1 [128kB]
-Get:12 http://ftp.uk.debian.org/debian/ sid/main libunistring0 alpha 0.9.3-3 [447kB]
-Get:13 http://ftp.uk.debian.org/debian/ sid/main gettext alpha 0.18.1.1-3 [2218kB]
-Get:14 http://ftp.uk.debian.org/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:15 http://ftp.uk.debian.org/debian/ sid/main po-debconf all 1.0.16 [224kB]
-Get:16 http://ftp.uk.debian.org/debian/ sid/main debhelper all 8.0.0 [454kB]
-Get:17 http://ftp.uk.debian.org/debian/ sid/main cdbs all 0.4.89 [1240kB]
-Get:18 http://ftp.uk.debian.org/debian/ sid/main zlib1g-dev alpha 1:1.2.3.4.dfsg-3 [206kB]
+ cdbs zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.9MB in 7s (1529kB/s)
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 9979 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_alpha.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_alpha.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_alpha.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_alpha.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_alpha.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_alpha.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_alpha.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_alpha.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_alpha.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_alpha.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_alpha.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_alpha.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_alpha.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+0 upgraded, 2 newly installed, 0 to remove and 57 not upgraded.
+Need to get 0 B/1446 kB of archives.
+After this operation, 2179 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
+(Reading database ... 13772 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_alpha.deb) ...
-Setting up bsdmainutils (8.0.13) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Processing triggers for man-db ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-Kernel: Linux 2.6.32-bpo.5-alpha-generic alpha (alpha)
-Toolchain package versions: libc6.1-dev_2.11.2-5 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-21 gcc-4.4_4.4.4-13 g++-4.4_4.4.4-13 binutils_2.20.1-14 libstdc++6-4.4-dev_4.4.4-13 libstdc++6_4.4.4-13
-Package versions: apt_0.8.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-14 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-5 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-13 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-13 gcc_4:4.4.4-2 gcc-4.4_4.4.4-13 gcc-4.4-base_4.4.4-13 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-5 libc-bin_2.11.2-5 libc-dev-bin_2.11.2-5 libc6.1_2.11.2-5 libc6.1-dev_2.11.2-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-13 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-13 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-2 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-13 libstdc++6-4.4-dev_4.4.4-13 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.1 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-21 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-2 netbase_4.42 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010l-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.26-2-alpha-generic alpha (alpha)
+Toolchain package versions: libc6.1-dev_2.11.2-8 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.10 asciidoc_8.5.2-1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 binutils-dev_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-2 cpp-4.3_4.3.5-3 cpp-4.4_4.4.5-10 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.4 diffutils_1:3.0-1 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.3_4.3.5-3 gcc-4.3-base_4.3.5-3 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-2 gettext-base_0.18.1.1-2 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-7 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-8 libc-dev-bin_2.11.2-8 libc6.1_2.11.2-8 libc6.1-dev_2.11.2-8 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-10 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.4 libelf-dev_0.148-1 libelf1_0.148-1 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libsqlite3-0_3.7.4-2 libss2_1.41.12-2 libssl0.9.8_0.9.8o-4 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 libxml2-utils_2.7.7.dfsg-4 libxslt1.1_1.1.26-6 linux-libc-dev_2.6.32-30 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 module-init-tools_3.12-1 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16 python_2.6.6-3+squeeze5 python-minimal_2.6.6-3+squeeze5 python2.6_2.6.6-8+b1 python2.6-minimal_2.6.6-8+b1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 sgml-data_2.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2.1 tzdata_2011a-1 util-linux_2.17.2-3.1 xml-core_0.13 xmlto_0.0.23-2 xsltproc_1.1.26-6 xz-utils_4.999.9beta+20100713-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -365,12 +136,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -385,36 +156,36 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture alpha
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -436,12 +207,13 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+ /usr/bin/fakeroot debian/rules binary-arch
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-alpha-RA1JNc/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- /usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -451,7 +223,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -481,63 +253,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_alpha.deb'.
- dpkg-genchanges -B -malpha Build Daemon (goetz) <buildd_alpha-goetz at buildd.debian.org> >../bwa_0.5.8c-1_alpha.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_alpha.deb'.
+ dpkg-genchanges -B -mDebian Build Daemon <buildd_alpha-goedel at buildd.debian.org> >../bwa_0.5.9-1_alpha.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-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1241
+Build finished at 20110208-1119
-bwa_0.5.8c-1_alpha.changes:
+bwa_0.5.9-1_alpha.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: alpha
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
-Maintainer: alpha Build Daemon (goetz) <buildd_alpha-goetz at buildd.debian.org>
+Maintainer: Debian Build Daemon <buildd_alpha-goedel at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- 7cd8dd2879f221b791b431518c8935a5d5c68c3e 155732 bwa_0.5.8c-1_alpha.deb
+ 7bac348943c694fc753bc9c66fbcdb9b9d90e9dc 161460 bwa_0.5.9-1_alpha.deb
Checksums-Sha256:
- 636e78c95d508bd38ab1542d67cb82f8bd36806d86ef64f03d5a5d17cc55687b 155732 bwa_0.5.8c-1_alpha.deb
+ bfabc531d5e68bab76e120df80400fda5f184cf9db06cc25215b144252cdb7e8 161460 bwa_0.5.9-1_alpha.deb
Files:
- dae39e0ca78ddba68d427b75c8c64b07 155732 science optional bwa_0.5.8c-1_alpha.deb
+ a6e4708ac6d5aaccf3bfdd82579463d6 161460 science optional bwa_0.5.9-1_alpha.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_alpha.deb
-──────────────────────
+bwa_0.5.9-1_alpha.deb
+─────────────────────
new debian package, version 2.0.
- size 155732 bytes: control archive= 945 bytes.
- 777 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 161460 bytes: control archive= 973 bytes.
+ 776 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: alpha
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 356
+ Installed-Size: 364
Depends: libc6.1 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -551,24 +320,25 @@ bwa_0.5.8c-1_alpha.deb
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 2010-10-27 12:41 ./
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/bin/
--rwxr-xr-x root/root 241368 2010-10-27 12:41 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/doc/bwa/
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:41 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/bwa/
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 11:19 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 11:19 ./usr/bin/
+-rwxr-xr-x root/root 249688 2011-02-08 11:19 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -577,9 +347,12 @@ drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/bwa/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-alpha-sbuild-35e99b14-4f1f-47f6-9875-7e8ad7b7d7b2/build/buildd-bwa_0.5.8c-1-alpha-bAhjmR
-Not removing build depends: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-alpha-sbuild-33a5461a-cb7a-41b3-85a6-02c69a43ad38/build/buildd-bwa_0.5.9-1-alpha-RA1JNc
+(Reading database ... 13852 files and directories currently installed.)
+Removing cdbs ...
+Removing zlib1g-dev ...
+Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1241
-Build needed 00:03:05, 3192k disc space
+Finished at 20110208-1119
+Build needed 00:01:34, 3244k disc space
diff --git a/armel.log b/armel.log
index cb773cf..6836120 100644
--- a/armel.log
+++ b/armel.log
@@ -1,4 +1,4 @@
-From buildd at ancina.debian.org Wed Oct 27 12:40:25 2010
+From buildd at ancina.debian.org Tue Feb 08 11:22:18 2011
Return-path: <buildd at ancina.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,37 +6,37 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at ancina.debian.org>)
- id 1PB5Im-0004om-QM
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:40:25 +0000
+ id 1PmleD-0006xl-Lo
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 11:22:17 +0000
Received: from ancina.ugent.be ([157.193.39.13] helo=ancina.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=ancina.debian.org, EMAIL=hostmaster at ancina.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at ancina.debian.org>)
- id 1PB5Ib-0004ZL-FB; Wed, 27 Oct 2010 12:40:13 +0000
+ id 1PmleC-0005IH-Oe; Tue, 08 Feb 2011 11:22:16 +0000
Received: from buildd by ancina.debian.org with local (Exim 4.69)
(envelope-from <buildd at ancina.debian.org>)
- id 1PB5IV-0003nf-JY; Wed, 27 Oct 2010 12:40:07 +0000
+ id 1Pmle7-0002RE-2X; Tue, 08 Feb 2011 11:22:11 +0000
From: Build Daemon <buildd at ancina.debian.org>
To: nchip at kos.to, logs at buildd.debian.org, zumbi at kos.to
-Subject: Log for successful build of bwa_0.5.8c-1 on armel (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on armel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PB5IV-0003nf-JY at ancina.debian.org>
-Date: Wed, 27 Oct 2010 12:40:07 +0000
+Message-Id: <E1Pmle7-0002RE-2X at ancina.debian.org>
+Date: Tue, 08 Feb 2011 11:22:11 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on ancina.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (armel) 27 Oct 2010 12:37 ║
+║ bwa 0.5.9-1 (armel) 08 Feb 2011 11:19 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: armel
-Chroot Build Dir: /var/lib/schroot/mount/sid-armel-sbuild-658792fe-eb4f-44cf-b522-9dbb20be863b/build/buildd-bwa_0.5.8c-1-armel-SPBlLP
-Start Time: 20101027-1237
+Chroot Build Dir: /var/lib/schroot/mount/sid-armel-sbuild-c0cc5792-ce4c-46e8-99a7-f7302d614395/build/buildd-bwa_0.5.9-1-armel-ykOV5b
+Start Time: 20110208-1119
Hit http://ftp.de.debian.org sid Release.gpg
Ign http://ftp.de.debian.org/debian/ sid/contrib Translation-en
Ign http://ftp.de.debian.org/debian/ sid/main Translation-en
@@ -44,21 +44,20 @@ Hit http://ftp.de.debian.org sid Release
Hit http://incoming.debian.org sid Release.gpg
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:1 http://incoming.debian.org Release.gpg [835B]
+Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org Release.gpg
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
Hit http://incoming.debian.org sid Release
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
-Get:2 http://incoming.debian.org Release [1604B]
Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
+Hit http://incoming.debian.org Release
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
Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
-Get:3 http://incoming.debian.org Sources [23.4kB]
-Get:4 http://incoming.debian.org Packages [85.4kB]
-Fetched 111kB in 7s (15.1kB/s)
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,20 +76,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 0s (162kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 0s (165 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -99,16 +98,13 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- udev libssl0.9.8
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
file gettext gettext-base groff-base html2text intltool-debian libcroco3
libglib2.0-0 libmagic1 libunistring0 libxml2 man-db po-debconf
@@ -123,14 +119,14 @@ The following NEW packages will be installed:
intltool-debian libcroco3 libglib2.0-0 libmagic1 libunistring0 libxml2
man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 16 newly installed, 0 to remove and 35 not upgraded.
-Need to get 0B/9281kB of archives.
-After this operation, 26.2MB of additional disk space will be used.
+0 upgraded, 16 newly installed, 0 to remove and 26 not upgraded.
+Need to get 0 B/9382 kB of archives.
+After this operation, 26.5 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 10725 files and directories currently installed.)
+(Reading database ... 10747 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_armel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_armel.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_armel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_armel.deb) ...
Selecting previously deselected package file.
@@ -138,7 +134,7 @@ Unpacking file (from .../archives/file_5.04-5_armel.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_armel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -152,35 +148,35 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_armel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-21 gcc-4.4_4.4.5-3 g++-4.4_4.4.5-3 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-3 libstdc++6_4.4.5-3
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-3 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dmsetup_2:1.02.48-3 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-3 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-3 gcc-4.4-base_4.4.5-3 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-3 libdpkg-perl_1.15.8.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-3 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-3 libgpg-error0_1.6-1 libgpm2_1.20.4-3.3 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-4 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libssl0.9.8_0.9.8o-2 libstdc++6_4.4.5-3 libstdc++6-4.4-dev_4.4.5-3 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_161-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libvolume-id1_0.141-2 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-21 login_1:4.1.4.2-1+b2 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 netbase_4.42 nullmailer_1:1.04-1.2 passwd_1:4.1.4.2-1+b2 patch_2.6-2 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 procps_1:3.2.8-9 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010m-1 udev_161-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-8 dpkg-dev_1.15.8.8 linux-libc-dev_2.6.32-29 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.10 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.2.1 bsdutils_1:2.17.2-6 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-6 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.37 debconf-i18n_1.5.37 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.2 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.8 dpkg-dev_1.15.8.8 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-6 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-8 libc-dev-bin_2.11.2-8 libc6_2.11.2-8 libc6-dev_2.11.2-8 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-10 libdb4.8_4.8.30-4 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.8 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libgpm2_1.20.4-3.3 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libssl0.9.8_0.9.8o-4 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_164-4 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-29 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-6 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 netbase_4.44 nullmailer_1:1.04-1.2 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-5 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011a-1 util-linux_2.17.2-6 wget_1.12-2.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -192,12 +188,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -212,36 +208,36 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture armel
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -263,9 +259,10 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-armel-SPBlLP/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-armel-ykOV5b/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -278,7 +275,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -308,63 +305,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bwa_0.5.8c-1_armel.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1240
+Build finished at 20110208-1122
-bwa_0.5.8c-1_armel.changes:
+bwa_0.5.9-1_armel.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: armel
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: armel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- 425bd0b34edd76306b105145f8a46d053185bdac 136056 bwa_0.5.8c-1_armel.deb
+ 0bcc3678f4793d1b4b1618ab646fd1b89f3ad236 140592 bwa_0.5.9-1_armel.deb
Checksums-Sha256:
- fb6de6ab60a90b2b1f225f0e58a719eb1f78ed87853a3949b26a0a7cf50a4a7c 136056 bwa_0.5.8c-1_armel.deb
+ 8749b51249b9ac15e0a250be501c8106b8b60e30c2c2b8897873df9893c1efff 140592 bwa_0.5.9-1_armel.deb
Files:
- 978d41512b178e321ea39440115a82eb 136056 science optional bwa_0.5.8c-1_armel.deb
+ 2974d95b03ff4f1fe633ed6f7cb07da7 140592 science optional bwa_0.5.9-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_armel.deb
-──────────────────────
+bwa_0.5.9-1_armel.deb
+─────────────────────
new debian package, version 2.0.
- size 136056 bytes: control archive= 943 bytes.
- 775 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 140592 bytes: control archive= 975 bytes.
+ 774 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 308
+ Installed-Size: 316
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -378,24 +372,25 @@ bwa_0.5.8c-1_armel.deb
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 2010-10-27 12:39 ./
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/bin/
--rwxr-xr-x root/root 190276 2010-10-27 12:39 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:39 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/bwa/
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./usr/bin/
+-rwxr-xr-x root/root 198360 2011-02-08 11:21 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 11:21 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./usr/share/bwa/
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 11:21 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -404,8 +399,8 @@ drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/doc/bwa/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-658792fe-eb4f-44cf-b522-9dbb20be863b/build/buildd-bwa_0.5.8c-1-armel-SPBlLP
-(Reading database ... 11920 files and directories currently installed.)
+Purging /var/lib/schroot/mount/sid-armel-sbuild-c0cc5792-ce4c-46e8-99a7-f7302d614395/build/buildd-bwa_0.5.9-1-armel-ykOV5b
+(Reading database ... 11983 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -431,6 +426,6 @@ Purging configuration files for libxml2 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1240
-Build needed 00:02:40, 2428k disc space
+Finished at 20110208-1122
+Build needed 00:02:30, 2464k disc space
diff --git a/hppa.log b/hppa.log
index 48d8965..879719f 100644
--- a/hppa.log
+++ b/hppa.log
@@ -1,4 +1,4 @@
-From buildd at penalosa.debian.org Wed Oct 27 12:41:38 2010
+From buildd at penalosa.debian.org Tue Feb 08 10:04:16 2011
Return-path: <buildd at penalosa.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,60 +6,96 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at penalosa.debian.org>)
- id 1PB5Jy-000522-Ny
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:41:38 +0000
+ id 1PmkQh-0000g0-RU
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 10:04:16 +0000
Received: from penalosa.debian.org ([192.25.206.68])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=penalosa.debian.org,
EMAIL=hostmaster at penalosa.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at penalosa.debian.org>)
- id 1PB5Jx-0004dl-1m; Wed, 27 Oct 2010 12:41:37 +0000
+ id 1PmkQg-0002Px-8M; Tue, 08 Feb 2011 10:04:14 +0000
Received: from buildd by penalosa.debian.org with local (Exim 4.69)
(envelope-from <buildd at penalosa.debian.org>)
- id 1PB5Jv-0007mb-0d; Wed, 27 Oct 2010 12:41:35 +0000
+ id 1PmkQc-0002OX-Lz; Tue, 08 Feb 2011 10:04:10 +0000
From: buildd on penalosa <buildd at penalosa.debian.org>
To: dannf+buildd at dannf.org,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on hppa (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on hppa (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PB5Jv-0007mb-0d at penalosa.debian.org>
-Date: Wed, 27 Oct 2010 12:41:35 +0000
+Message-Id: <E1PmkQc-0002OX-Lz at penalosa.debian.org>
+Date: Tue, 08 Feb 2011 10:04:10 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on penalosa.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (hppa) 27 Oct 2010 12:38 ║
+║ bwa 0.5.9-1 (hppa) 08 Feb 2011 10:00 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: hppa
-Chroot Build Dir: /var/lib/schroot/mount/sid-hppa-sbuild-329697bc-0f29-40e4-b33f-4a177fafa474/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF
-Start Time: 20101027-1238
-Hit http://spohr.debian.org sid Release.gpg
+Chroot Build Dir: /var/lib/schroot/mount/sid-hppa-sbuild-adf641b4-c3b2-44bf-801b-b6f703ce29e4/build/buildd-bwa_0.5.9-1-hppa-BksjZx
+Start Time: 20110208-1000
+Get:1 http://spohr.debian.org sid Release.gpg [835 B]
Ign http://spohr.debian.org/debian/ sid/contrib Translation-en
Ign http://spohr.debian.org/debian/ sid/main Translation-en
-Hit http://spohr.debian.org sid Release
-Hit http://spohr.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid Release.gpg
+Get:2 http://spohr.debian.org sid Release [104 kB]
+Get:3 http://incoming.debian.org sid Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:1 http://incoming.debian.org Release.gpg [835B]
+Get:4 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://spohr.debian.org sid/contrib Sources/DiffIndex
-Hit http://spohr.debian.org sid/main hppa Packages/DiffIndex
-Hit http://spohr.debian.org sid/contrib hppa Packages/DiffIndex
-Hit http://incoming.debian.org sid Release
-Get:2 http://incoming.debian.org Release [1604B]
-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 hppa Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib hppa Packages/DiffIndex
-Get:3 http://incoming.debian.org Sources [23.4kB]
-Get:4 http://incoming.debian.org Packages [85.4kB]
-Fetched 111kB in 6s (18.4kB/s)
+Get:5 http://incoming.debian.org sid Release [104 kB]
+Get:6 http://spohr.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:7 http://incoming.debian.org Release [1604 B]
+Get:8 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:9 http://spohr.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:10 http://spohr.debian.org sid/main hppa Packages/DiffIndex [2038 B]
+Get:11 http://spohr.debian.org sid/contrib hppa Packages/DiffIndex [2023 B]
+Get:12 http://spohr.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:13 http://spohr.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:14 http://spohr.debian.org sid/main hppa 2011-02-08-0211.24.pdiff [23.3 kB]
+Get:15 http://incoming.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:16 http://incoming.debian.org sid/main hppa Packages/DiffIndex [2038 B]
+Get:17 http://spohr.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:18 http://spohr.debian.org sid/contrib hppa 2011-02-08-0211.24.pdiff [300 B]
+Get:19 http://incoming.debian.org sid/contrib hppa Packages/DiffIndex [2023 B]
+Get:20 http://incoming.debian.org Sources [43.7 kB]
+Get:21 http://incoming.debian.org Packages [683 kB]
+Get:22 http://incoming.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:23 http://incoming.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:24 http://incoming.debian.org sid/main hppa 2011-02-08-0211.24.pdiff [23.3 kB]
+Get:25 http://spohr.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:26 http://spohr.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:27 http://spohr.debian.org sid/main hppa 2011-02-08-0211.24.pdiff [23.3 kB]
+Get:28 http://spohr.debian.org sid/contrib hppa 2011-02-08-0211.24.pdiff [300 B]
+Get:29 http://incoming.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:30 http://incoming.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:31 http://incoming.debian.org sid/contrib hppa 2011-02-08-0211.24.pdiff [300 B]
+Get:32 http://incoming.debian.org sid/main hppa 2011-02-08-0211.24.pdiff [23.3 kB]
+Get:33 http://incoming.debian.org sid/contrib hppa 2011-02-08-0211.24.pdiff [300 B]
+Get:34 http://spohr.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:35 http://spohr.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:36 http://spohr.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:37 http://spohr.debian.org sid/main hppa 2011-02-08-0211.24.pdiff [23.3 kB]
+Get:38 http://spohr.debian.org sid/contrib hppa 2011-02-08-0211.24.pdiff [300 B]
+Get:39 http://incoming.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:40 http://spohr.debian.org sid/main hppa 2011-02-08-0812.10.pdiff [19.8 kB]
+Get:41 http://spohr.debian.org sid/main hppa 2011-02-08-0812.10.pdiff [19.8 kB]
+Get:42 http://incoming.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:43 http://incoming.debian.org sid/main hppa 2011-02-08-0211.24.pdiff [23.3 kB]
+Get:44 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:45 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:46 http://incoming.debian.org sid/contrib hppa 2011-02-08-0211.24.pdiff [300 B]
+Get:47 http://spohr.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:48 http://incoming.debian.org sid/main hppa 2011-02-08-0812.10.pdiff [19.8 kB]
+Get:49 http://incoming.debian.org sid/main hppa 2011-02-08-0812.10.pdiff [19.8 kB]
+Get:50 http://spohr.debian.org sid/main hppa 2011-02-08-0812.10.pdiff [19.8 kB]
+Get:51 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:52 http://incoming.debian.org sid/main hppa 2011-02-08-0812.10.pdiff [19.8 kB]
+Fetched 1076 kB in 33s (32.3 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,20 +114,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 0s (180kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 7s (15.6 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -100,7 +136,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -120,21 +156,23 @@ The following NEW packages will be installed:
cdbs debhelper gettext gettext-base groff-base html2text intltool-debian
libcroco3 libglib2.0-0 libpcre3 libunistring0 libxml2 man-db po-debconf
zlib1g-dev
+0 upgraded, 15 newly installed, 0 to remove and 27 not upgraded.
+Need to get 263 kB/10.0 MB of archives.
+After this operation, 26.3 MB of additional disk space will be used.
+Get:1 http://spohr.debian.org/debian/ sid/main libpcre3 hppa 8.12-1 [263 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 15 newly installed, 0 to remove and 18 not upgraded.
-Need to get 0B/9891kB of archives.
-After this operation, 26.0MB of additional disk space will be used.
+Fetched 263 kB in 5s (43.9 kB/s)
Selecting previously deselected package groff-base.
-(Reading database ... 11683 files and directories currently installed.)
+(Reading database ... 11565 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_hppa.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_hppa.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_hppa.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hppa.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_hppa.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-1_hppa.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_hppa.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_hppa.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_hppa.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -148,34 +186,34 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_hppa.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hppa.deb) ...
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libpcre3 (8.12-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-5-parisc64 hppa (parisc64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.5-2 g++-4.4_4.4.5-2 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-2 libstdc++6_4.4.5-2
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dmsetup_2:1.02.48-3 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-3 libdpkg-perl_1.15.8.5 libextutils-parsexs-perl_2.220600-1 libgc1c2_1:6.8-1.2 libgcc4_4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmodule-build-perl_0.360700-1 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline-dev_6.1-3 libreadline5_5.2-7 libreadline6_6.1-3 libreadline6-dev_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4+b1 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_163-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 libyaml-perl_0.71-1 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 procps_1:3.2.8-9 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tcl8.4_8.4.19-4 tzdata_2010l-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.6 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.10.3 base-files_5.10 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-5 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.3 debconf_1.5.37 debconf-i18n_1.5.37 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.2 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.6 dpkg-dev_1.15.8.6 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-7 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-10 libc-dev-bin_2.11.2-10 libc6_2.11.2-10 libc6-dev_2.11.2-10 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-10 libdb4.8_4.8.30-4 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.6 libextutils-parsexs-perl_2.220600-1 libgc1c2_1:6.8-1.2 libgcc4_4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmodule-build-perl_0.360700-1 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.12-1 libpng12-0_1.2.44-1 libreadline5_5.2-7 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4+b1 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_164-4 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 libyaml-perl_0.71-1 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-5 sysv-rc_2.88dsf-13 sysvinit_2.88dsf-13 sysvinit-utils_2.88dsf-13 tar_1.25-3 tzdata_2010o-1 util-linux_2.17.2-3.3 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -187,12 +225,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -207,36 +245,36 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture hppa
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -258,9 +296,10 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-hppa-BksjZx/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -273,7 +312,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -303,63 +342,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_hppa.deb'.
- dpkg-genchanges -B -mhppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd.debian.org> >../bwa_0.5.8c-1_hppa.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_hppa.deb'.
+ dpkg-genchanges -B -mhppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd.debian.org> >../bwa_0.5.9-1_hppa.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-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1241
+Build finished at 20110208-1003
-bwa_0.5.8c-1_hppa.changes:
+bwa_0.5.9-1_hppa.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: hppa
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: hppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- 41c292c9766bca6ecff2d629938dffe2e22a23fc 143948 bwa_0.5.8c-1_hppa.deb
+ 5f06f4df53421a315b9ed18bbc2e6ad8f570862b 150112 bwa_0.5.9-1_hppa.deb
Checksums-Sha256:
- f881664710b08004531132fb7e4ba6a9d1a0cb4dce32a77787325cbe6cfc9772 143948 bwa_0.5.8c-1_hppa.deb
+ 11bf49e74b9288873f38c3ddc6f779bbe7e0faef75d4956857276ad98596ac92 150112 bwa_0.5.9-1_hppa.deb
Files:
- 2f5ac9630002f9d1a22170941f6f7518 143948 science optional bwa_0.5.8c-1_hppa.deb
+ c99e9162416bc4686e6236935641fe0c 150112 science optional bwa_0.5.9-1_hppa.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_hppa.deb
-─────────────────────
+bwa_0.5.9-1_hppa.deb
+────────────────────
new debian package, version 2.0.
- size 143948 bytes: control archive= 943 bytes.
- 775 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 150112 bytes: control archive= 970 bytes.
+ 774 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: hppa
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 316
+ Installed-Size: 324
Depends: libc6 (>= 2.11), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -373,24 +409,25 @@ bwa_0.5.8c-1_hppa.deb
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 2010-10-27 12:41 ./
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/bin/
--rwxr-xr-x root/root 197436 2010-10-27 12:41 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/doc/bwa/
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:41 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./usr/bin/
+-rwxr-xr-x root/root 205380 2011-02-08 10:03 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 10:03 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 10:03 ./usr/share/man/man1/bwa.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -399,8 +436,8 @@ drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/man/man1/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-hppa-sbuild-329697bc-0f29-40e4-b33f-4a177fafa474/build/buildd-bwa_0.5.8c-1-hppa-ZCTKKF
-(Reading database ... 12863 files and directories currently installed.)
+Purging /var/lib/schroot/mount/sid-hppa-sbuild-adf641b4-c3b2-44bf-801b-b6f703ce29e4/build/buildd-bwa_0.5.9-1-hppa-BksjZx
+(Reading database ... 12786 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -425,6 +462,6 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1241
-Build needed 00:02:24, 2540k disc space
+Finished at 20110208-1003
+Build needed 00:02:56, 2580k disc space
diff --git a/hurd-i386.log b/hurd-i386.log
index fe22929..b7d7c5a 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,38 +1,38 @@
-From buildd at mozart.debian.net Wed Oct 27 16:12:49 2010
-Return-path: <buildd at mozart.debian.net>
+From buildd at bach.debian.net Tue Feb 08 09:15:20 2011
+Return-path: <buildd at bach.debian.net>
Received: from callisto.debian.net ([80.87.129.151])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at mozart.debian.net>)
- id 1PB8cL-00059t-0I
- for logs at buildd.debian.org; Wed, 27 Oct 2010 16:12:49 +0000
-Received: from mozart.debian.net ([10.1.0.1])
+ (Exim 4.69) (envelope-from <buildd at bach.debian.net>)
+ id 1PmjfM-000562-1O
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 09:15:20 +0000
+Received: from bach.debian.net ([10.3.0.1])
by callisto.debian.net with esmtp (Exim 4.69)
- (envelope-from <buildd at mozart.debian.net>)
- id 1PB8cH-0004sg-6L; Wed, 27 Oct 2010 17:12:45 +0100
-Received: from buildd by mozart.debian.net with local (Exim 4.72)
- (envelope-from <buildd at mozart.debian.net>)
- id 1PB8cF-0005P3-Gk; Wed, 27 Oct 2010 16:12:43 +0000
-Date: Wed, 27 Oct 2010 16:12:43 +0000
-Message-Id: <E1PB8cF-0005P3-Gk at mozart.debian.net>
-From: Build Daemon <buildd at mozart.debian.net>
+ (envelope-from <buildd at bach.debian.net>)
+ id 1PmjfK-0004na-1C; Tue, 08 Feb 2011 09:15:18 +0000
+Received: from buildd by bach.debian.net with local (Exim 4.72)
+ (envelope-from <buildd at bach.debian.net>)
+ id 1PmjfN-0004eP-Po; Tue, 08 Feb 2011 09:15:23 +0000
+Date: Tue, 08 Feb 2011 09:15:21 +0000
+Message-Id: <E1PmjfN-0004eP-Po at bach.debian.net>
+From: Build Daemon <buildd at bach.debian.net>
To: samuel.thibault at labri.fr, mbanck at gmx.net, logs at debian-ports.org,
logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on hurd-i386 (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 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) 0.59.1 (31 Jan 2010) on mozart.debian.net
+sbuild (Debian sbuild) 0.59.1 (31 Jan 2010) on bach.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (hurd-i386) 27 Oct 2010 16:10 ║
+║ bwa 0.5.9-1 (hurd-i386) 08 févr. 2011 09:02 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-unstable/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa
-Start Time: 20101027-1610
+Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8
+Start Time: 20110208-0902
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -44,26 +44,80 @@ Check APT
Checking available source versions...
+Update APT
+──────────
+
+Ign file: ./ Release.gpg
+Ign file:/build/local-debs/ ./ Translation-en
+Ign file: ./ Release
+Ign file: ./ Packages
+Get:1 http://ftp.debian-ports.org unreleased Release.gpg [835 B]
+Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
+Get:2 http://ftp.debian-ports.org unreleased Release [17.4 kB]
+Get:3 http://incoming.debian.org Release.gpg [835 B]
+Ign http://incoming.debian.org/buildd-unstable/ Translation-en
+Get:4 http://incoming.debian.org Release [1604 B]
+Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Get:5 http://incoming.debian.org Sources [43.1 kB]
+Get:6 http://ftp.uk.debian.org sid Release.gpg [835 B]
+Ign http://ftp.uk.debian.org/debian/ sid/contrib Translation-en
+Ign http://ftp.uk.debian.org/debian/ sid/main Translation-en
+Ign http://ftp.uk.debian.org/debian/ sid/non-free Translation-en
+Get:7 http://ftp.uk.debian.org sid Release [104 kB]
+Get:8 http://incoming.debian.org Packages [680 kB]
+Get:9 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
+Get:10 http://ftp.uk.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:11 http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
+Get:12 http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex [2023 B]
+Get:13 http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex [2023 B]
+Get:14 http://ftp.uk.debian.org sid/main 2011-02-07-2014.05.pdiff [30.3 kB]
+Get:15 http://ftp.uk.debian.org sid/main 2011-02-07-2014.05.pdiff [30.3 kB]
+Get:16 http://ftp.uk.debian.org sid/main 2011-02-07-2014.05.pdiff [30.3 kB]
+Get:17 http://ftp.uk.debian.org sid/non-free 2011-02-07-2014.05.pdiff [235 B]
+Get:18 http://ftp.uk.debian.org sid/non-free 2011-02-07-2014.05.pdiff [235 B]
+Get:19 http://ftp.uk.debian.org sid/main hurd-i386 2011-02-07-2014.05.pdiff [104 kB]
+Get:20 http://ftp.uk.debian.org sid/main hurd-i386 2011-02-07-2014.05.pdiff [104 kB]
+Get:21 http://ftp.uk.debian.org sid/contrib hurd-i386 2011-02-07-2014.05.pdiff [719 B]
+Get:22 http://ftp.uk.debian.org sid/contrib hurd-i386 2011-02-07-2014.05.pdiff [719 B]
+Get:23 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-02-07-2014.05.pdiff [42 B]
+Get:24 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-02-07-2014.05.pdiff [42 B]
+Get:25 http://ftp.uk.debian.org sid/non-free 2011-02-07-2014.05.pdiff [235 B]
+Get:26 http://ftp.uk.debian.org sid/main hurd-i386 2011-02-07-2014.05.pdiff [104 kB]
+Ign http://ftp.uk.debian.org sid/main 2011-02-08-0211.24.pdiff
+Ign http://ftp.uk.debian.org sid/non-free 2011-02-08-0211.24.pdiff
+Get:27 http://ftp.uk.debian.org sid/main [4117 kB]
+Get:28 http://ftp.uk.debian.org sid/non-free [83.8 kB]
+Get:29 http://ftp.uk.debian.org sid/contrib hurd-i386 2011-02-07-2014.05.pdiff [719 B]
+Get:30 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-02-07-2014.05.pdiff [42 B]
+Fetched 5195 kB in 4min 21s (19.9 kB/s)
+W: Failed to fetch http://ftp.uk.debian.org/debian/dists/sid/main/source/Sources.bz2 Hash Sum mismatch
+
+W: Failed to fetch http://ftp.uk.debian.org/debian/dists/sid/non-free/source/Sources.bz2 Hash Sum mismatch
+
+E: Some index files failed to download, they have been ignored, or old ones used instead.
+Checking available source versions...
+
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 0s (132kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 0s (140 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -71,39 +125,41 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
-debhelper: already installed (8.0.0 >= 7 is satisfied)
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+debhelper: already installed (8.0.0 >= 8 is satisfied)
+zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies: cdbs
+Installing positive dependencies: cdbs zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libwrap0 libcwidget3 libsigc++-2.0-0c2a libxapian15 libboost-iostreams1.42.0
- adduser libsysfs2
+ libpopt0 libwrap0 libsysfs2 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
Suggested packages:
devscripts doc-base
Recommended packages:
autotools-dev
The following NEW packages will be installed:
- cdbs
-0 upgraded, 1 newly installed, 0 to remove and 21 not upgraded.
-Need to get 0B/1240kB of archives.
-After this operation, 1696kB of additional disk space will be used.
+ cdbs zlib1g-dev
+0 upgraded, 2 newly installed, 0 to remove and 48 not upgraded.
+Need to get 0 B/1426 kB of archives.
+After this operation, 2114 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- cdbs
+ cdbs zlib1g-dev
Authentication warning overridden.
Selecting previously deselected package cdbs.
-(Reading database ... 14198 files and directories currently installed.)
+(Reading database ... 12173 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Selecting previously deselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
Processing triggers for man-db ...
Setting up cdbs (0.4.89) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: libc0.3-dev_2.11.2-6 dpkg-dev_1.15.8.5 hurd-dev_20100926-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-5 g++-4.4_4.4.5-5 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-5 libstdc++6_4.4.5-5
-Package versions: adduser_3.112+nmu1 apt_0.8.5 apt-utils_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-5 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 deborphan_1.7.28 dialog_1.1-20100428-1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.4-2 g++-4.4_4.4.5-5 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.4_4.4.5-5 gcc-4.4-base_4.4.5-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnumach_2:1.3.99.dfsg.git20100732-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 hurd_20100926-1 hurd-dev_20100926-1 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libapt-pkg-dev_0.8.5 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libboost-iostreams1.42.0_1.42.0-4 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc0.3_2.11.2-6 libc0.3-dev_2.11.2-6 libc0.3-xen_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libept-dev_1.0.3+b2 libept1_1.0.3+b2 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.2-2 libgcc1_1:4.4.5-5 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.5-2 libgomp1_4.4.5-5 libgpg-error0_1.6-1 libidn11_1.18-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.03-5+b1 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libparted0debian1_2.3-1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-5.1 libsasl2-modules_2.1.23.dfsg1-5.1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-2 libstdc++6_4.4.5-5 libstdc++6-4.4-dev_4.4.5-5 libsysfs2_2.1.0+repack-1 libtagcoll2-dev_2.0.11-1.1 libtasn1-3_2.7-1 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libuuid1_2.16.2-0 libwibble-dev_0.1.26-1 libwrap0_7.6.dbs-8 libxapian-dev_1.2.3-2 libxapian15_1.0.20-2 libxapian22_1.2.3-2 libxml2_2.7.7.dfsg-4 lsb-base_3.2-25 lynx-cur_2.8.8dev.5-1 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 pkg-config_0.25-1 po-debconf_1.0.16 procps_1:3.2.7-11 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-3 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-dejavu-core_2.31-1 type-handling_0.2.23 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.16.2-0 xml-core_0.13 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc0.3-dev_2.11.2-10 dpkg-dev_1.15.8.5 hurd-dev_20100926-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: adduser_3.112+nmu1 apt_0.8.10 apt-utils_0.8.10 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsd-mailx_8.1.2-0.20100314cvs-1 bsdmainutils_8.0.13 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 cron_3.0pl1-116 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_3.4.1 deborphan_1.7.28 dialog_1.1-20100428-1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 exim4-base_4.72-3+b1 exim4-config_4.72-3 exim4-daemon-light_4.72-3+b1 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.4-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnumach_2:1.3.99.dfsg.git20100732-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 hurd_20100926-1 hurd-dev_20100926-1 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-10 libc-dev-bin_2.11.2-10 libc0.3_2.11.2-10 libc0.3-dev_2.11.2-10 libc0.3-xen_2.11.2-10 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.2-2.1 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.5-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblockfile1_1.08-4 liblzma2_5.0.0-2 libmagic1_5.03-5+b1 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libparted0debian1_2.3-3+hurd.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-5.1 libsasl2-modules_2.1.23.dfsg1-5.1 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-4 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwrap0_7.6.dbs-8 libxml2_2.7.8.dfsg-2 lsb-base_3.2-25 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-5 netbase_4.42 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16 procps_1:3.2.7-11 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-3 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-bitstream-vera_1.10-8 ttf-dejavu-core_2.31-1 ttf-freefont_20090104-7 type-handling_0.2.23 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.16.2-0 xml-core_0.13 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -115,12 +171,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -129,42 +185,42 @@ Check disc space
dpkg-buildpackage
─────────────────
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -186,9 +242,10 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8/bwa-0.5.9'
touch debian/stamp-makefile-build
/usr/bin/fakeroot debian/rules binary-arch
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -201,7 +258,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -231,63 +288,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../bwa_0.5.8c-1_hurd-i386.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1612
+Build finished at 20110208-0914
-bwa_0.5.8c-1_hurd-i386.changes:
+bwa_0.5.9-1_hurd-i386.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: hurd-i386
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- e54e4327c2f33c90317b46feb333ef0ecf4b9880 133344 bwa_0.5.8c-1_hurd-i386.deb
+ 4b28106f861e69300a8b4d464954f14b389884bd 139252 bwa_0.5.9-1_hurd-i386.deb
Checksums-Sha256:
- cdce2d4c752c3b1f523a10307eac866f0a547a45ce3d858cb0b4f94ce1ece01e 133344 bwa_0.5.8c-1_hurd-i386.deb
+ e5601502543cdb55f9f9ea08d5602bd7d20e911c61d379c1e42a6662a4d24daa 139252 bwa_0.5.9-1_hurd-i386.deb
Files:
- 98230712cfaaee7cf0d0a1c951a32d99 133344 science optional bwa_0.5.8c-1_hurd-i386.deb
+ 87b2a6eae61da3b27224c95fef6326c2 139252 science optional bwa_0.5.9-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_hurd-i386.deb
-──────────────────────────
+bwa_0.5.9-1_hurd-i386.deb
+─────────────────────────
new debian package, version 2.0.
- size 133344 bytes: control archive= 953 bytes.
- 788 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 139252 bytes: control archive= 984 bytes.
+ 787 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 312
+ Installed-Size: 320
Depends: hurd, libc0.3 (>= 2.11), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -301,24 +355,25 @@ bwa_0.5.8c-1_hurd-i386.deb
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 2010-10-27 16:12 ./
-drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 16:12 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/bin/
--rwxr-xr-x root/root 194352 2010-10-27 16:12 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 09:13 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 09:13 ./usr/bin/
+-rwxr-xr-x root/root 202576 2011-02-08 09:13 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -327,11 +382,12 @@ drwxr-xr-x root/root 0 2010-10-27 16:12 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-unstable/build/buildd-bwa_0.5.8c-1-hurd-i386-MlnFqa
-(Reading database ... 14254 files and directories currently installed.)
+Purging /home/buildd/build/chroot-sid/build/buildd-bwa_0.5.9-1-hurd-i386-GXKWi8
+(Reading database ... 12259 files and directories currently installed.)
Removing cdbs ...
+Removing zlib1g-dev ...
Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1612
-Build needed 00:01:47, 2420k disc space
+Finished at 20110208-0914
+Build needed 00:12:15, 2440k disc space
diff --git a/i386.log b/i386.log
index f3d0be2..b4e4c46 100644
--- a/i386.log
+++ b/i386.log
@@ -1,4 +1,4 @@
-From buildd at biber.debian.org Wed Oct 27 12:42:07 2010
+From buildd at biber.debian.org Tue Feb 08 09:00:22 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,
@@ -6,61 +6,61 @@ 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 4.69) (envelope-from <buildd at biber.debian.org>)
- id 1PB5KQ-000597-Re
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:42:07 +0000
+ id 1PmjQr-0003vA-M9
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 09:00:21 +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 4.69) (envelope-from <buildd at biber.debian.org>)
- id 1PB5KP-00075r-DD; Wed, 27 Oct 2010 12:42:05 +0000
+ id 1PmjQq-0002Mt-4e; Tue, 08 Feb 2011 09:00:20 +0000
Received: from buildd by biber.debian.org with local (Exim 4.69)
(envelope-from <buildd at biber.debian.org>)
- id 1PB5KP-0006BM-VG; Wed, 27 Oct 2010 12:42:05 +0000
+ id 1PmjQp-00048v-1Y; Tue, 08 Feb 2011 09:00:19 +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 bwa_0.5.8c-1 on i386 (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on i386 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PB5KP-0006BM-VG at biber.debian.org>
-Date: Wed, 27 Oct 2010 12:42:05 +0000
+Message-Id: <E1PmjQp-00048v-1Y at biber.debian.org>
+Date: Tue, 08 Feb 2011 09:00:19 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (i386) 27 Oct 2010 12:40 ║
+║ bwa 0.5.9-1 (i386) 08 Feb 2011 08:58 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: i386
-Chroot Build Dir: /var/lib/schroot/mount/sid-i386-sbuild-88a29433-d8ec-4562-abe0-bbbf1ca59adf/build/buildd-bwa_0.5.8c-1-i386-kKgEpp
-Start Time: 20101027-1240
-Get:1 http://ftp.gr.debian.org unstable Release.gpg [835B]
+Chroot Build Dir: /var/lib/schroot/mount/sid-i386-sbuild-946b0c24-fbad-4f1f-8340-f0459f369c02/build/buildd-bwa_0.5.9-1-i386-GDa6n4
+Start Time: 20110208-0858
+Get:1 http://ftp.gr.debian.org unstable Release.gpg [835 B]
Ign http://ftp.gr.debian.org/debian/ unstable/contrib Translation-en
Ign http://ftp.gr.debian.org/debian/ unstable/main Translation-en
-Get:2 http://ftp.gr.debian.org unstable Release [104kB]
-Get:3 http://ftp.gr.debian.org unstable/main Sources [4008kB]
-Get:4 http://incoming.debian.org unstable Release.gpg [835B]
+Get:2 http://ftp.gr.debian.org unstable Release [104 kB]
+Get:3 http://ftp.gr.debian.org unstable/main Sources [4117 kB]
+Get:4 http://incoming.debian.org unstable Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:5 http://ftp.gr.debian.org unstable/contrib Sources [38.7kB]
-Get:6 http://ftp.gr.debian.org unstable/non-free Sources [80.3kB]
-Get:7 http://ftp.gr.debian.org unstable/main i386 Packages [6857kB]
-Get:8 http://incoming.debian.org Release.gpg [835B]
+Get:5 http://ftp.gr.debian.org unstable/contrib Sources [38.6 kB]
+Get:6 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:9 http://incoming.debian.org unstable Release [104kB]
-Get:10 http://ftp.gr.debian.org unstable/contrib i386 Packages [60.6kB]
-Get:11 http://incoming.debian.org Release [1604B]
-Get:12 http://incoming.debian.org unstable/main Sources [4008kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [80.3kB]
-Get:15 http://incoming.debian.org unstable/main i386 Packages [6857kB]
-Get:16 http://incoming.debian.org unstable/contrib i386 Packages [60.6kB]
-Get:17 http://incoming.debian.org Sources [23.4kB]
-Get:18 http://incoming.debian.org Packages [85.4kB]
-Fetched 22.4MB in 20s (1092kB/s)
+Get:7 http://incoming.debian.org unstable Release [104 kB]
+Get:8 http://ftp.gr.debian.org unstable/non-free Sources [83.8 kB]
+Get:9 http://ftp.gr.debian.org unstable/main i386 Packages [6996 kB]
+Get:10 http://ftp.gr.debian.org unstable/contrib i386 Packages [60.6 kB]
+Get:11 http://incoming.debian.org Release [1604 B]
+Get:12 http://incoming.debian.org unstable/main Sources [4119 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [38.6 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [83.8 kB]
+Get:15 http://incoming.debian.org unstable/main i386 Packages [6996 kB]
+Get:16 http://incoming.debian.org unstable/contrib i386 Packages [60.6 kB]
+Get:17 http://incoming.debian.org Sources [43.1 kB]
+Get:18 http://incoming.debian.org Packages [680 kB]
+Fetched 23.5 MB in 20s (1154 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -79,20 +79,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 1s (116kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 1s (110 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -101,7 +101,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -122,36 +122,36 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 50 not upgraded.
-Need to get 9824kB of archives.
-After this operation, 27.7MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.0.13 [198kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.20.1-10 [1128kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.5.7-6 [1240kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.02-1.1 [231kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.7.dfsg-4 [827kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.24.2-1 [1029kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16 [224kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186kB]
+0 upgraded, 18 newly installed, 0 to remove and 3 not upgraded.
+Need to get 9948 kB of archives.
+After this operation, 28.0 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.2 [200 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.20.1-10 [1128 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.5.7-8 [1240 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-1 [255 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-2 [827 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.24.2-1 [1029 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.1.0 [552 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
+Get:18 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 9824kB in 1s (9727kB/s)
+Fetched 9948 kB in 0s (11.8 MB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10126 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_i386.deb) ...
+(Reading database ... 10198 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_i386.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_i386.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_i386.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_i386.deb) ...
Selecting previously deselected package file.
@@ -159,9 +159,9 @@ Unpacking file (from .../archives/file_5.04-5_i386.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_i386.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-1_i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -175,39 +175,39 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libpcre3 (8.12-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.26-2-amd64 i386 (x86_64)
-Toolchain package versions: libc6-dev_2.11.2-5 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-21 gcc-4.4_4.4.4-13 g++-4.4_4.4.4-13 binutils_2.20.1-14 libstdc++6-4.4-dev_4.4.4-13 libstdc++6_4.4.4-13
-Package versions: apt_0.8.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-14 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-5 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-13 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-13 gcc_4:4.4.4-2 gcc-4.4_4.4.4-13 gcc-4.4-base_4.4.4-13 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-5 libc-bin_2.11.2-5 libc-dev-bin_2.11.2-5 libc6_2.11.2-5 libc6-dev_2.11.2-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-13 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-13 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-2 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-13 libstdc++6-4.4-dev_4.4.4-13 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.1 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-21 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-2 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010l-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.10.3 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.12-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011a-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -219,12 +219,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -239,36 +239,36 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture 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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -290,9 +290,10 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-i386-kKgEpp/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-i386-GDa6n4/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -305,7 +306,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -335,63 +336,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bwa_0.5.8c-1_i386.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1242
+Build finished at 20110208-0900
-bwa_0.5.8c-1_i386.changes:
+bwa_0.5.9-1_i386.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: i386
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- 7b39edd345cec332e65c65199f168c60ae64633a 134156 bwa_0.5.8c-1_i386.deb
+ 7cc69d2a2f59bf0d52dc0a0eb8b304847cd07705 139584 bwa_0.5.9-1_i386.deb
Checksums-Sha256:
- 776088668475ca978908c4600d8f2abd777d4ac47df20fd064cf8ab605b5b965 134156 bwa_0.5.8c-1_i386.deb
+ 488bec898fba7878d5302659f86f8906b9bc69584d6aed850de49ab115611a77 139584 bwa_0.5.9-1_i386.deb
Files:
- 38d48ae9c0c4dcdd606ead9eaebe4e08 134156 science optional bwa_0.5.8c-1_i386.deb
+ 73a8c24f0fa3aff8b8666460637bff08 139584 science optional bwa_0.5.9-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_i386.deb
-─────────────────────
+bwa_0.5.9-1_i386.deb
+────────────────────
new debian package, version 2.0.
- size 134156 bytes: control archive= 945 bytes.
- 774 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 139584 bytes: control archive= 975 bytes.
+ 773 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 312
+ Installed-Size: 320
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -405,24 +403,25 @@ bwa_0.5.8c-1_i386.deb
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 2010-10-27 12:42 ./
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/bin/
--rwxr-xr-x root/root 194352 2010-10-27 12:42 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:42 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/bwa/
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./usr/bin/
+-rwxr-xr-x root/root 202576 2011-02-08 09:00 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 09:00 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 09:00 ./usr/share/bwa/
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -431,8 +430,9 @@ drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/bwa/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-i386-sbuild-88a29433-d8ec-4562-abe0-bbbf1ca59adf/build/buildd-bwa_0.5.8c-1-i386-kKgEpp
+Purging /var/lib/schroot/mount/sid-i386-sbuild-946b0c24-fbad-4f1f-8340-f0459f369c02/build/buildd-bwa_0.5.9-1-i386-GDa6n4
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1242
+Finished at 20110208-0900
+Build needed 00:02:15, 2444k disc space
diff --git a/ia64.log b/ia64.log
index ce251c2..a0e46c3 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,4 +1,4 @@
-From buildd at caballero.debian.org Wed Oct 27 12:39:18 2010
+From buildd at caballero.debian.org Tue Feb 08 09:00:03 2011
Return-path: <buildd at caballero.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,61 +6,67 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at caballero.debian.org>)
- id 1PB5Hi-0004m2-8k
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:39:18 +0000
+ id 1PmjQY-0003r4-Np
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 09:00:03 +0000
Received: from caballero.debian.org ([193.201.200.200])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=caballero.debian.org,
EMAIL=hostmaster at caballero.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at caballero.debian.org>)
- id 1PB5Hg-0004Z1-5Q; Wed, 27 Oct 2010 12:39:17 +0000
+ id 1PmjQX-0008Pk-Je; Tue, 08 Feb 2011 09:00:01 +0000
Received: from buildd by caballero.debian.org with local (Exim 4.69)
- (envelope-from <buildd at caballero.debian.org>) id 1PB5Hf-0002U7-CZ
- for buildd-porters at caballero.debian.org; Wed, 27 Oct 2010 12:39:15 +0000
+ (envelope-from <buildd at caballero.debian.org>) id 1PmjQV-0004NH-Be
+ for buildd-porters at caballero.debian.org; Tue, 08 Feb 2011 08:59:59 +0000
From: buildd on caballero <buildd at caballero.debian.org>
To: buildd-porters at caballero.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on ia64 (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PB5Hf-0002U7-CZ at caballero.debian.org>
-Date: Wed, 27 Oct 2010 12:39:15 +0000
+Message-Id: <E1PmjQV-0004NH-Be at caballero.debian.org>
+Date: Tue, 08 Feb 2011 08:59:59 +0000
Delivered-To: buildd-porters at caballero.debian.org
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on caballero.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (ia64) 27 Oct 2010 12:37 ║
+║ bwa 0.5.9-1 (ia64) 08 Feb 2011 08:58 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: ia64
-Chroot Build Dir: /var/lib/schroot/mount/sid-ia64-sbuild-80649626-769c-4b76-a086-ddd09985a201/build/buildd-bwa_0.5.8c-1-ia64-XinPyh
-Start Time: 20101027-1237
+Chroot Build Dir: /var/lib/schroot/mount/sid-ia64-sbuild-7b6e40ef-fd0d-4cc6-b286-8894c01872bf/build/buildd-bwa_0.5.9-1-ia64-mYX4RF
+Start Time: 20110208-0858
Hit http://mirror.positive-internet.com sid Release.gpg
Ign http://mirror.positive-internet.com/debian/ sid/contrib Translation-en
Ign http://mirror.positive-internet.com/debian/ sid/main Translation-en
Hit http://mirror.positive-internet.com sid Release
Hit http://mirror.positive-internet.com sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid Release.gpg
+Get:1 http://incoming.debian.org sid Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:1 http://incoming.debian.org Release.gpg [835B]
+Get:2 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
Hit http://mirror.positive-internet.com sid/contrib Sources/DiffIndex
Hit http://mirror.positive-internet.com sid/main ia64 Packages/DiffIndex
Hit http://mirror.positive-internet.com sid/contrib ia64 Packages/DiffIndex
-Hit http://incoming.debian.org sid Release
-Get:2 http://incoming.debian.org Release [1604B]
+Get:3 http://incoming.debian.org sid Release [104 kB]
+Get:4 http://incoming.debian.org Release [1604 B]
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 ia64 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
-Get:3 http://incoming.debian.org Sources [23.4kB]
-Get:4 http://incoming.debian.org Packages [85.4kB]
-Fetched 111kB in 4s (22.7kB/s)
+Get:5 http://incoming.debian.org Sources [43.1 kB]
+Get:6 http://incoming.debian.org Packages [680 kB]
+Get:7 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:8 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:9 http://incoming.debian.org sid/main ia64 2011-02-08-0812.10.pdiff [1593 B]
+Get:10 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:11 http://incoming.debian.org sid/main ia64 2011-02-08-0812.10.pdiff [1593 B]
+Get:12 http://incoming.debian.org sid/main ia64 2011-02-08-0812.10.pdiff [1593 B]
+Fetched 731 kB in 8s (84.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -79,20 +85,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 0s (219kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 0s (212 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -101,7 +107,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -122,20 +128,20 @@ The following NEW packages will be installed:
libcroco3 libglib2.0-0 libpcre3 libunistring0 libxml2 man-db po-debconf
zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 15 newly installed, 0 to remove and 19 not upgraded.
-Need to get 0B/11.8MB of archives.
-After this operation, 37.1MB of additional disk space will be used.
+0 upgraded, 15 newly installed, 0 to remove and 41 not upgraded.
+Need to get 0 B/11.9 MB of archives.
+After this operation, 37.4 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 10381 files and directories currently installed.)
+(Reading database ... 10389 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_ia64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_ia64.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_ia64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_ia64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_ia64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -149,34 +155,34 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_ia64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: libc6.1-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.5-5 g++-4.4_4.4.5-5 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-5 libstdc++6_4.4.5-5
-Package versions: apt_0.8.5 autoconf_2.67-2 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-5 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-5 gcc_4:4.4.5-1 gcc-4.4_4.4.5-5 gcc-4.4-base_4.4.5-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6.1_2.11.2-6 libc6.1-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-5 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-5 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.5-5 libstdc++6-4.4-dev_4.4.5-5 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 lzma_4.43-14 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010m-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6.1-dev_2.11.2-8 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.10.3 autoconf_2.67-2 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-7 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-8 libc-dev-bin_2.11.2-8 libc6.1_2.11.2-8 libc6.1-dev_2.11.2-8 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-3 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 lzma_4.43-14 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2011a-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -188,12 +194,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -208,36 +214,36 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture ia64
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -259,9 +265,10 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-ia64-XinPyh/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-ia64-mYX4RF/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -274,7 +281,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -304,63 +311,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../bwa_0.5.8c-1_ia64.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1239
+Build finished at 20110208-0859
-bwa_0.5.8c-1_ia64.changes:
+bwa_0.5.9-1_ia64.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: ia64
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- a52c0843d14193bb914c939df8535a23f4d14170 198812 bwa_0.5.8c-1_ia64.deb
+ 3e2cd190f2a5c9127845be41bd867eaaf58aea7b 206904 bwa_0.5.9-1_ia64.deb
Checksums-Sha256:
- 92895030f56a2d3ab8bc49524c2d8cb824058de119aa4240bf23911b3ef6a2ce 198812 bwa_0.5.8c-1_ia64.deb
+ 990e3f6606a6fa6bc29b910f13c7a78ee83955135288517d88136fd827c1e442 206904 bwa_0.5.9-1_ia64.deb
Files:
- 6f2355ed69c0ad4b12e43dbe4376a83a 198812 science optional bwa_0.5.8c-1_ia64.deb
+ dac1bf8adcbb484689b4a142ce0fbf3a 206904 science optional bwa_0.5.9-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_ia64.deb
-─────────────────────
+bwa_0.5.9-1_ia64.deb
+────────────────────
new debian package, version 2.0.
- size 198812 bytes: control archive= 944 bytes.
- 776 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 206904 bytes: control archive= 976 bytes.
+ 775 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 520
+ Installed-Size: 536
Depends: libc6.1 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -374,24 +378,25 @@ bwa_0.5.8c-1_ia64.deb
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 2010-10-27 12:39 ./
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:39 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/bin/
--rwxr-xr-x root/root 405832 2010-10-27 12:39 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 08:59 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 08:59 ./usr/bin/
+-rwxr-xr-x root/root 422872 2011-02-08 08:59 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -400,8 +405,8 @@ drwxr-xr-x root/root 0 2010-10-27 12:39 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-80649626-769c-4b76-a086-ddd09985a201/build/buildd-bwa_0.5.8c-1-ia64-XinPyh
-(Reading database ... 11567 files and directories currently installed.)
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-7b6e40ef-fd0d-4cc6-b286-8894c01872bf/build/buildd-bwa_0.5.9-1-ia64-mYX4RF
+(Reading database ... 11610 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -426,6 +431,6 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1239
-Build needed 00:01:12, 3556k disc space
+Finished at 20110208-0859
+Build needed 00:01:17, 3636k disc space
diff --git a/info b/info
index 8960cfc..1eaf64d 100644
--- a/info
+++ b/info
@@ -1,13 +1,13 @@
-powerpc~1288183131~unstable~successful
-ia64~1288183159~unstable~successful
-armel~1288183225~unstable~successful
-sparc~1288183247~unstable~successful
-hppa~1288183299~unstable~successful
-s390~1288183300~unstable~successful
-alpha~1288183303~unstable~successful
-i386~1288183327~unstable~successful
-kfreebsd-i386~1288183352~unstable~successful
-hurd-i386~1288195969~unstable~successful
-kfreebsd-amd64~1288212465~unstable~successful
-mipsel~1288314914~unstable~successful
-mips~1288367809~unstable~successful
+ia64~1297155605~sid~successful
+i386~1297155622~sid~successful
+kfreebsd-amd64~1297155831~sid~successful
+powerpc~1297155837~sid~successful
+kfreebsd-i386~1297155935~sid~successful
+hurd-i386~1297156521~sid~successful
+hppa~1297159466~sid~successful
+alpha~1297163981~sid~successful
+armel~1297164138~sid~successful
+mipsel~1297172751~sid~successful
+sparc~1297173593~sid~successful
+s390~1297197328~sid~successful
+mips~1297414295~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index d1b2e50..c42623f 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,4 +1,4 @@
-From buildd at fano.debian.org Wed Oct 27 20:47:44 2010
+From buildd at fano.debian.org Tue Feb 08 09:03:51 2011
Return-path: <buildd at fano.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,
@@ -6,23 +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 4.69) (envelope-from <buildd at fano.debian.org>)
- id 1PBCuO-0001uy-Dg
- for logs at buildd.debian.org; Wed, 27 Oct 2010 20:47:44 +0000
+ id 1PmjUE-0004Cd-Mt
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 09:03:50 +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=hostmaster at fano.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at fano.debian.org>)
- id 1PBCuM-0000ps-KP; Wed, 27 Oct 2010 20:47:43 +0000
+ id 1PmjUC-0002SH-VH; Tue, 08 Feb 2011 09:03:49 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1PBCuK-000AHT-2k; Wed, 27 Oct 2010 20:47:40 +0000
-Date: Wed, 27 Oct 2010 20:47:40 +0000
-Message-Id: <E1PBCuK-000AHT-2k at fano.debian.org>
+ id 1PmjUA-0007Jz-DL; Tue, 08 Feb 2011 09:03:46 +0000
+Date: Tue, 08 Feb 2011 09:03:46 +0000
+Message-Id: <E1PmjUA-0007Jz-DL at fano.debian.org>
From: buildd on fano <buildd at fano.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
-Subject: Log for successful build of bwa_0.5.8c-1 on kfreebsd-amd64
- (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on kfreebsd-amd64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -30,32 +29,43 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (kfreebsd-amd64) 27 Oct 2010 20:46 ║
+║ bwa 0.5.9-1 (kfreebsd-amd64) 08 Feb 2011 09:02 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: kfreebsd-amd64
-Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX
-Start Time: 20101027-2046
+Chroot Build Dir: /var/lib/schroot/mount/sid-ka-sbuild-1297155760-27067/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy
+Start Time: 20110208-0902
Hit http://ftp.ca.debian.org sid Release.gpg
-Hit http://incoming.debian.org sid Release.gpg
+Get:1 http://incoming.debian.org sid Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
Ign http://ftp.ca.debian.org/debian/ sid/main Translation-en
Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Hit http://incoming.debian.org Release.gpg
+Get:2 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://incoming.debian.org sid Release
+Get:3 http://incoming.debian.org sid Release [104 kB]
Hit http://ftp.ca.debian.org sid Release
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
Hit http://ftp.ca.debian.org sid/main Sources/DiffIndex
+Get:4 http://incoming.debian.org Release [1604 B]
+Hit http://ftp.ca.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Get:5 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
+Get:6 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
-Hit http://incoming.debian.org Packages
-Hit http://ftp.ca.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Get:7 http://incoming.debian.org Sources [43.1 kB]
+Get:8 http://incoming.debian.org Packages [680 kB]
+Get:9 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:10 http://incoming.debian.org sid/main kfreebsd-amd64 2011-02-08-0812.10.pdiff [35.8 kB]
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
+Get:11 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:12 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:13 http://incoming.debian.org sid/main kfreebsd-amd64 2011-02-08-0812.10.pdiff [35.8 kB]
+Get:14 http://incoming.debian.org sid/main kfreebsd-amd64 2011-02-08-0812.10.pdiff [35.8 kB]
+Fetched 873 kB in 7s (118 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,20 +84,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120 kB of source archives.
-Get:1 http://ftp.ca.debian.org/debian/ sid/main bwa 0.5.8c-1 (dsc) [1905 B]
-Get:2 http://ftp.ca.debian.org/debian/ sid/main bwa 0.5.8c-1 (tar) [114 kB]
-Get:3 http://ftp.ca.debian.org/debian/ sid/main bwa 0.5.8c-1 (diff) [4005 B]
-Fetched 120 kB in 0s (127 kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 0s (145 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -96,7 +106,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -110,21 +120,21 @@ Suggested packages:
devscripts doc-base dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
+debconf: delaying package configuration, since apt-utils is not installed
autotools-dev 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 file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
libxml2 man-db po-debconf zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 17 newly installed, 0 to remove and 11 not upgraded.
-Need to get 0 B/10.2 MB of archives.
-After this operation, 26.8 MB of additional disk space will be used.
+0 upgraded, 17 newly installed, 0 to remove and 2 not upgraded.
+Need to get 0 B/10.3 MB of archives.
+After this operation, 27.1 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 11774 files and directories currently installed.)
+(Reading database ... 11819 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-amd64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_kfreebsd-amd64.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_kfreebsd-amd64.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-amd64.deb) ...
Selecting previously deselected package file.
@@ -132,9 +142,9 @@ Unpacking file (from .../file_5.04-5_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_kfreebsd-amd64.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_kfreebsd-amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -148,36 +158,36 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-amd64.deb) ...
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libpcre3 (8.12-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-4 gcc-4.4_4.4.5-4 g++-4.4_4.4.5-4 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-4 libc0.1-dev_2.11.2-6 kfreebsd-kernel-headers_0.53
-Package versions: apt_0.8.7 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-4 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-2+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-4 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-4 gcc-4.4-base_4.4.5-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc0.1_2.11.2-6 libc0.1-dev_2.11.2-6 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-4 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-4 libgpg-error0_1.6-1 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-4 libstdc++6-4.4-dev_4.4.5-4 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 procps_1:3.2.8-9 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 type-handling_0.2.23 tzdata_2010m-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.10 libstdc++6_4.4.5-10 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libc0.1-dev_2.11.2-11 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.10.3 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-6 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.3+b1 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1+b1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc0.1_2.11.2-11 libc0.1-dev_2.11.2-11 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.12-1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011a-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -189,12 +199,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -209,36 +219,36 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture kfreebsd-amd64
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -260,9 +270,10 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -275,7 +286,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -305,63 +316,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bwa_0.5.8c-1_kfreebsd-amd64.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-2047
+Build finished at 20110208-0903
-bwa_0.5.8c-1_kfreebsd-amd64.changes:
+bwa_0.5.9-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: kfreebsd-amd64
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- f91f8d750824b9d231bec5efe60d7d4fac98808f 131674 bwa_0.5.8c-1_kfreebsd-amd64.deb
+ 0800bb7f5d51d07083d2b78243e729343fe087ca 137390 bwa_0.5.9-1_kfreebsd-amd64.deb
Checksums-Sha256:
- be64d2145be4ec6a7f269868766a2d2a41c24b9b50460a7c93c2c1696c3af472 131674 bwa_0.5.8c-1_kfreebsd-amd64.deb
+ 95c5c011bb7d2c71d8d6cc9bfae79f280a8416ddf2aab533fe76b9bdcbd97f4d 137390 bwa_0.5.9-1_kfreebsd-amd64.deb
Files:
- cd1f2c974ce8617facd6408719053f91 131674 science optional bwa_0.5.8c-1_kfreebsd-amd64.deb
+ 7bc054e6b524c35eadb49d88a23f00ea 137390 science optional bwa_0.5.9-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_kfreebsd-amd64.deb
-───────────────────────────────
+bwa_0.5.9-1_kfreebsd-amd64.deb
+──────────────────────────────
new debian package, version 2.0.
- size 131674 bytes: control archive= 949 bytes.
- 786 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 137390 bytes: control archive= 983 bytes.
+ 785 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 268
+ Installed-Size: 276
Depends: libc0.1 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -375,24 +383,25 @@ bwa_0.5.8c-1_kfreebsd-amd64.deb
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 2010-10-27 20:47 ./
-drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 20:47 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/bin/
--rwxr-xr-x root/root 187464 2010-10-27 20:47 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 09:03 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/bin/
+-rwxr-xr-x root/root 195688 2011-02-08 09:03 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -401,8 +410,8 @@ drwxr-xr-x root/root 0 2010-10-27 20:47 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-bwa_0.5.8c-1-kfreebsd-amd64-5rtgAX
-(Reading database ... 12983 files and directories currently installed.)
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1297155760-27067/build/buildd-bwa_0.5.9-1-kfreebsd-amd64-96K9Uy
+(Reading database ... 13069 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -430,6 +439,6 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-2047
-Build needed 00:00:41, 2634k disc space
+Finished at 20110208-0903
+Build needed 00:00:53, 2696k disc space
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index e14e624..aebe628 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,70 +1,76 @@
-From buildd at finzi.debian.org Wed Oct 27 12:42:32 2010
-Return-path: <buildd at finzi.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at field.debian.org Tue Feb 08 09:05:34 2011
+Return-path: <buildd at field.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
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 4.69) (envelope-from <buildd at finzi.debian.org>)
- id 1PB5Kq-0005AV-4u
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:42:32 +0000
-Received: from finzi.debian.org ([206.12.19.111])
+ (Exim 4.69) (envelope-from <buildd at field.debian.org>)
+ id 1PmjVu-0004V2-K6
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 09:05:34 +0000
+Received: from field.debian.org ([194.177.211.210])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at finzi.debian.org>)
- id 1PB5Ko-00075y-D3; Wed, 27 Oct 2010 12:42:31 +0000
-Received: from buildd by finzi.debian.org with local (Exim 4.72)
- (envelope-from <buildd at finzi.debian.org>)
- id 1PB5Kl-0001DM-Hl; Wed, 27 Oct 2010 12:42:27 +0000
-Date: Wed, 27 Oct 2010 12:42:27 +0000
-Message-Id: <E1PB5Kl-0001DM-Hl at finzi.debian.org>
-From: buildd on finzi <buildd at finzi.debian.org>
+ CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at field.debian.org>)
+ id 1PmjVt-0000EC-4T; Tue, 08 Feb 2011 09:05:33 +0000
+Received: from buildd by field.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at field.debian.org>)
+ id 1PmjVr-000Q0F-NB; Tue, 08 Feb 2011 09:05:31 +0000
+Date: Tue, 08 Feb 2011 09:05:31 +0000
+Message-Id: <E1PmjVr-000Q0F-NB at field.debian.org>
+From: buildd on field <buildd at field.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
-Subject: Log for successful build of bwa_0.5.8c-1 on kfreebsd-i386
- (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on kfreebsd-i386 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on finzi.debian.org
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (kfreebsd-i386) 27 Oct 2010 12:41 ║
+║ bwa 0.5.9-1 (kfreebsd-i386) 08 Feb 2011 09:03 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: kfreebsd-i386
-Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB
-Start Time: 20101027-1241
-Hit http://incoming.debian.org sid Release.gpg
+Chroot Build Dir: /var/lib/schroot/mount/sid-ki-sbuild-1297155812-98383/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b
+Start Time: 20110208-0903
+Hit http://ftp.gr.debian.org sid Release.gpg
+Ign http://ftp.gr.debian.org/debian/ sid/contrib Translation-en
+Ign http://ftp.gr.debian.org/debian/ sid/main Translation-en
+Ign http://ftp.gr.debian.org/debian/ sid/non-free Translation-en
+Hit http://ftp.gr.debian.org sid Release
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Get:1 http://incoming.debian.org sid Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Hit http://ftp.ca.debian.org sid Release.gpg
-Ign http://ftp.ca.debian.org/debian/ sid/contrib Translation-en
-Ign http://ftp.ca.debian.org/debian/ sid/main Translation-en
-Ign http://ftp.ca.debian.org/debian/ sid/non-free Translation-en
Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Hit http://incoming.debian.org Release.gpg
+Get:2 http://incoming.debian.org Release.gpg [835 B]
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://incoming.debian.org sid Release
-Hit http://ftp.ca.debian.org sid Release
-Hit http://incoming.debian.org Release
-Hit http://ftp.ca.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Get:3 http://incoming.debian.org sid Release [104 kB]
+Get:4 http://incoming.debian.org Release [1604 B]
+Get:5 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
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-i386 Packages/DiffIndex
+Get:6 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.ca.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.ca.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.ca.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.ca.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.ca.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
+Get:7 http://incoming.debian.org Sources [43.1 kB]
+Get:8 http://incoming.debian.org Packages [680 kB]
+Get:9 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:10 http://incoming.debian.org sid/main kfreebsd-i386 2011-02-08-0812.10.pdiff [46.7 kB]
+Get:11 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:12 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:13 http://incoming.debian.org sid/main kfreebsd-i386 2011-02-08-0812.10.pdiff [46.7 kB]
+Get:14 http://incoming.debian.org sid/main kfreebsd-i386 2011-02-08-0812.10.pdiff [46.7 kB]
+Fetched 884 kB in 7s (115 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,20 +89,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (dsc) [1905 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (tar) [114 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (diff) [4005 B]
-Fetched 120 kB in 0s (145 kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 1s (95.3 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -105,7 +111,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -119,21 +125,21 @@ Suggested packages:
devscripts doc-base dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev 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 file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
libxml2 man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 17 newly installed, 0 to remove and 7 not upgraded.
-Need to get 0 B/9516 kB of archives.
-After this operation, 25.1 MB of additional disk space will be used.
+0 upgraded, 17 newly installed, 0 to remove and 2 not upgraded.
+Need to get 0 B/9638 kB of archives.
+After this operation, 25.4 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 13368 files and directories currently installed.)
+(Reading database ... 11764 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_kfreebsd-i386.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-i386.deb) ...
Selecting previously deselected package file.
@@ -141,9 +147,9 @@ Unpacking file (from .../file_5.04-5_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_kfreebsd-i386.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -157,36 +163,36 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-i386.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libpcre3 (8.12-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-Kernel: GNU/kFreeBSD 8.1-1-686 kfreebsd-i386 (i686)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-5 gcc-4.4_4.4.5-5 g++-4.4_4.4.5-5 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-5 libc0.1-dev_2.11.2-6 kfreebsd-kernel-headers_0.53
-Package versions: apt_0.8.7 autotools-dev_20100122.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-5 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-2+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-5 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-5 gcc-4.4-base_4.4.5-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc0.1_2.11.2-6 libc0.1-dev_2.11.2-6 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-5 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-5 libgpg-error0_1.6-1 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-5 libstdc++6-4.4-dev_4.4.5-5 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 procps_1:3.2.8-9 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 type-handling_0.2.23 tzdata_2010m-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 vim_2:7.3.000+hg~ee53a39d5896-1 vim-common_2:7.3.000+hg~ee53a39d5896-1 vim-runtime_2:7.3.000+hg~ee53a39d5896-1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.10 libstdc++6_4.4.5-10 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libc0.1-dev_2.11.2-11 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.10.3 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.3+b1 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1+b1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc0.1_2.11.2-11 libc0.1-dev_2.11.2-11 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.12-1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 netbase_4.45 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011a-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -198,12 +204,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -218,36 +224,36 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture kfreebsd-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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -269,9 +275,10 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -284,7 +291,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -314,63 +321,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bwa_0.5.8c-1_kfreebsd-i386.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1242
+Build finished at 20110208-0905
-bwa_0.5.8c-1_kfreebsd-i386.changes:
+bwa_0.5.9-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: kfreebsd-i386
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
+Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- f812568641093efa91f9758121551f0763c3cec9 133176 bwa_0.5.8c-1_kfreebsd-i386.deb
+ f85dc517c094f0095101c513cd0c58aceb75e6e0 139068 bwa_0.5.9-1_kfreebsd-i386.deb
Checksums-Sha256:
- 252e077611e9c74b02a128d4df0f1c2c54cc44b516512d24c7be7afcadfbbcc3 133176 bwa_0.5.8c-1_kfreebsd-i386.deb
+ 9edf76ef0deff8c372d18caa894fc3be2a8f1935628e4d93d20d3a256b7ee1c6 139068 bwa_0.5.9-1_kfreebsd-i386.deb
Files:
- f4eaa4bcf64dba1c8cd8c9e349d97f76 133176 science optional bwa_0.5.8c-1_kfreebsd-i386.deb
+ 934289b6921938bb9a14f4c76c385246 139068 science optional bwa_0.5.9-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_kfreebsd-i386.deb
-──────────────────────────────
+bwa_0.5.9-1_kfreebsd-i386.deb
+─────────────────────────────
new debian package, version 2.0.
- size 133176 bytes: control archive= 948 bytes.
- 785 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 139068 bytes: control archive= 982 bytes.
+ 784 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 274
+ Installed-Size: 308
Depends: libc0.1 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -384,24 +388,25 @@ bwa_0.5.8c-1_kfreebsd-i386.deb
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 2010-10-27 12:42 ./
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:42 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/bin/
--rwxr-xr-x root/root 194352 2010-10-27 12:42 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 09:05 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 09:05 ./usr/bin/
+-rwxr-xr-x root/root 202576 2011-02-08 09:05 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -410,8 +415,8 @@ drwxr-xr-x root/root 0 2010-10-27 12:42 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-bwa_0.5.8c-1-kfreebsd-i386-IAkvZB
-(Reading database ... 14575 files and directories currently installed.)
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1297155812-98383/build/buildd-bwa_0.5.9-1-kfreebsd-i386-TdDy_b
+(Reading database ... 13014 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -439,6 +444,6 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1242
-Build needed 00:00:46, 2216k disc space
+Finished at 20110208-0905
+Build needed 00:01:34, 2294k disc space
diff --git a/mips.log b/mips.log
index 943867b..bd3f34c 100644
--- a/mips.log
+++ b/mips.log
@@ -1,42 +1,42 @@
-From buildd at corelli.debian.org Fri Oct 29 15:56:49 2010
+From buildd at corelli.debian.org Fri Feb 11 08:51:35 2011
Return-path: <buildd at corelli.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+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 4.69) (envelope-from <buildd at corelli.debian.org>)
- id 1PBrJw-0003TT-Rc
- for logs at buildd.debian.org; Fri, 29 Oct 2010 15:56:49 +0000
+ id 1Pnoj0-0000Le-CD
+ for logs at buildd.debian.org; Fri, 11 Feb 2011 08:51:35 +0000
Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=corelli.debian.org, EMAIL=hostmaster at corelli.debian.org (verified)
- 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)
(Exim 4.69) (envelope-from <buildd at corelli.debian.org>)
- id 1PBrJu-0007ro-LA; Fri, 29 Oct 2010 15:56:47 +0000
+ id 1Pnoiy-0002jx-6x; Fri, 11 Feb 2011 08:51:33 +0000
Received: from buildd by corelli.debian.org with local (Exim 4.69)
(envelope-from <buildd at corelli.debian.org>)
- id 1PBrJs-0007oN-83; Fri, 29 Oct 2010 15:56:44 +0000
+ id 1Pnoiu-0005w9-Uv; Fri, 11 Feb 2011 08:51:29 +0000
From: buildd on corelli <buildd at corelli.debian.org>
To: aba at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on mips (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PBrJs-0007oN-83 at corelli.debian.org>
-Date: Fri, 29 Oct 2010 15:56:44 +0000
+Message-Id: <E1Pnoiu-0005w9-Uv at corelli.debian.org>
+Date: Fri, 11 Feb 2011 08:51:28 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on corelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (mips) 29 Oct 2010 15:50 ║
+║ bwa 0.5.9-1 (mips) 11 Feb 2011 08:45 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: mips
-Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-34058ea3-7a06-49e0-8dc2-9e8bff6ce7bc/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw
-Start Time: 20101029-1550
+Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-dc8f20d6-132a-41bf-8c89-51f580f2ad13/build/buildd-bwa_0.5.9-1-mips-rZRDcv
+Start Time: 20110211-0845
Get:1 http://mirrors.ece.ubc.ca unstable Release.gpg [835B]
Ign http://mirrors.ece.ubc.ca/debian/ unstable/contrib Translation-en
Ign http://mirrors.ece.ubc.ca/debian/ unstable/main Translation-en
@@ -44,23 +44,23 @@ Get:2 http://mirrors.ece.ubc.ca unstable Release [104kB]
Get:3 http://incoming.debian.org unstable Release.gpg [835B]
Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:4 http://mirrors.ece.ubc.ca unstable/main Sources [4011kB]
-Get:5 http://incoming.debian.org Release.gpg [835B]
+Get:4 http://incoming.debian.org Release.gpg [835B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:6 http://incoming.debian.org unstable Release [104kB]
+Get:5 http://incoming.debian.org unstable Release [104kB]
+Get:6 http://mirrors.ece.ubc.ca unstable/main Sources [4163kB]
Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4011kB]
-Get:9 http://mirrors.ece.ubc.ca unstable/contrib Sources [38.7kB]
-Get:10 http://mirrors.ece.ubc.ca unstable/non-free Sources [80.6kB]
-Get:11 http://mirrors.ece.ubc.ca unstable/main mips Packages [6656kB]
-Get:12 http://mirrors.ece.ubc.ca unstable/contrib mips Packages [51.5kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [80.6kB]
-Get:15 http://incoming.debian.org unstable/main mips Packages [6656kB]
-Get:16 http://incoming.debian.org unstable/contrib mips Packages [51.5kB]
-Get:17 http://incoming.debian.org Sources [10.0kB]
-Get:18 http://incoming.debian.org Packages [152kB]
-Fetched 22.0MB in 48s (451kB/s)
+Get:8 http://incoming.debian.org unstable/main Sources [4163kB]
+Get:9 http://mirrors.ece.ubc.ca unstable/contrib Sources [39.1kB]
+Get:10 http://mirrors.ece.ubc.ca unstable/non-free Sources [84.0kB]
+Get:11 http://mirrors.ece.ubc.ca unstable/main mips Packages [6782kB]
+Get:12 http://mirrors.ece.ubc.ca unstable/contrib mips Packages [50.8kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [39.1kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [84.0kB]
+Get:15 http://incoming.debian.org unstable/main mips Packages [6782kB]
+Get:16 http://incoming.debian.org unstable/contrib mips Packages [50.8kB]
+Get:17 http://incoming.debian.org Sources [44.1kB]
+Get:18 http://incoming.debian.org Packages [537kB]
+Fetched 23.0MB in 49s (464kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -79,20 +79,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120kB of source archives.
-Get:1 http://mirrors.ece.ubc.ca/debian/ unstable/main bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://mirrors.ece.ubc.ca/debian/ unstable/main bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://mirrors.ece.ubc.ca/debian/ unstable/main bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 0s (1520kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119kB of source archives.
+Get:1 http://mirrors.ece.ubc.ca/debian/ unstable/main bwa 0.5.9-1 (dsc) [1894B]
+Get:2 http://mirrors.ece.ubc.ca/debian/ unstable/main bwa 0.5.9-1 (tar) [114kB]
+Get:3 http://mirrors.ece.ubc.ca/debian/ unstable/main bwa 0.5.9-1 (diff) [3651B]
+Fetched 119kB in 0s (602kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -101,7 +101,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.1
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -110,8 +110,8 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
- po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff less www-browser libmail-box-perl
@@ -120,38 +120,41 @@ Recommended packages:
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
- libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 43 not upgraded.
-Need to get 10.0MB of archives.
-After this operation, 30.1MB of additional disk space will be used.
-Get:1 http://mirrors.ece.ubc.ca/debian/ unstable/main bsdmainutils mips 8.0.13 [207kB]
-Get:2 http://mirrors.ece.ubc.ca/debian/ unstable/main groff-base mips 1.20.1-10 [1190kB]
-Get:3 http://mirrors.ece.ubc.ca/debian/ unstable/main man-db mips 2.5.7-6 [1251kB]
-Get:4 http://mirrors.ece.ubc.ca/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
-Get:5 http://mirrors.ece.ubc.ca/debian/ unstable/main file mips 5.04-5 [49.7kB]
-Get:6 http://mirrors.ece.ubc.ca/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153kB]
-Get:7 http://mirrors.ece.ubc.ca/debian/ unstable/main libpcre3 mips 8.02-1.1 [232kB]
-Get:8 http://mirrors.ece.ubc.ca/debian/ unstable/main libxml2 mips 2.7.7.dfsg-4 [835kB]
-Get:9 http://mirrors.ece.ubc.ca/debian/ unstable/main html2text mips 1.3.2a-15 [103kB]
-Get:10 http://mirrors.ece.ubc.ca/debian/ unstable/main libglib2.0-0 mips 2.24.2-1 [1043kB]
-Get:11 http://mirrors.ece.ubc.ca/debian/ unstable/main libcroco3 mips 0.6.2-1 [110kB]
-Get:12 http://mirrors.ece.ubc.ca/debian/ unstable/main libunistring0 mips 0.9.3-3 [415kB]
-Get:13 http://mirrors.ece.ubc.ca/debian/ unstable/main gettext mips 0.18.1.1-3 [2037kB]
-Get:14 http://mirrors.ece.ubc.ca/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:15 http://mirrors.ece.ubc.ca/debian/ unstable/main po-debconf all 1.0.16 [224kB]
-Get:16 http://mirrors.ece.ubc.ca/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:17 http://mirrors.ece.ubc.ca/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:18 http://mirrors.ece.ubc.ca/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 19 newly installed, 0 to remove and 66 not upgraded.
+Need to get 9930kB of archives.
+After this operation, 29.9MB of additional disk space will be used.
+Get:1 http://mirrors.ece.ubc.ca/debian/ unstable/main bsdmainutils mips 8.2.2 [210kB]
+Get:2 http://mirrors.ece.ubc.ca/debian/ unstable/main groff-base mips 1.21-4 [1203kB]
+Get:3 http://mirrors.ece.ubc.ca/debian/ unstable/main libpipeline1 mips 1.1.0-1 [35.1kB]
+Get:4 http://mirrors.ece.ubc.ca/debian/ unstable/main man-db mips 2.5.9-4 [997kB]
+Get:5 http://mirrors.ece.ubc.ca/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
+Get:6 http://mirrors.ece.ubc.ca/debian/ unstable/main file mips 5.04-5 [49.7kB]
+Get:7 http://mirrors.ece.ubc.ca/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153kB]
+Get:8 http://mirrors.ece.ubc.ca/debian/ unstable/main libpcre3 mips 8.02-1.1 [232kB]
+Get:9 http://mirrors.ece.ubc.ca/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2 [837kB]
+Get:10 http://mirrors.ece.ubc.ca/debian/ unstable/main html2text mips 1.3.2a-15 [103kB]
+Get:11 http://mirrors.ece.ubc.ca/debian/ unstable/main libglib2.0-0 mips 2.24.2-1 [1043kB]
+Get:12 http://mirrors.ece.ubc.ca/debian/ unstable/main libcroco3 mips 0.6.2-1 [110kB]
+Get:13 http://mirrors.ece.ubc.ca/debian/ unstable/main libunistring0 mips 0.9.3-3 [415kB]
+Get:14 http://mirrors.ece.ubc.ca/debian/ unstable/main gettext mips 0.18.1.1-3 [2037kB]
+Get:15 http://mirrors.ece.ubc.ca/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
+Get:16 http://mirrors.ece.ubc.ca/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
+Get:17 http://mirrors.ece.ubc.ca/debian/ unstable/main debhelper all 8.1.1 [552kB]
+Get:18 http://mirrors.ece.ubc.ca/debian/ unstable/main cdbs all 0.4.92 [1268kB]
+Get:19 http://mirrors.ece.ubc.ca/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.0MB in 2s (4864kB/s)
+Fetched 9930kB in 3s (2887kB/s)
Selecting previously deselected package bsdmainutils.
(Reading database ... 10143 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_mips.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mips.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_mips.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_mips.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_mips.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_mips.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_mips.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_mips.deb) ...
Selecting previously deselected package file.
@@ -161,7 +164,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mips.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mips.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -175,39 +178,40 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.1_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
-Setting up cdbs (0.4.89) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.1) ...
+Setting up cdbs (0.4.92) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-22 gcc-4.4_4.4.4-14 g++-4.4_4.4.4-14 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-14 libstdc++6_4.4.4-14
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-5 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-14 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-14 gcc_4:4.4.4-2 gcc-4.4_4.4.4-14 gcc-4.4-base_4.4.4-14 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-5 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-14 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-14 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-3 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-14 libstdc++6-4.4-dev_4.4.4-14 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.1 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-22 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-3 netbase_4.42 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010l-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.2.2 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-5 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-14 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.1.1 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-14 gcc_4:4.4.4-2 gcc-4.4_4.4.4-14 gcc-4.4-base_4.4.4-14 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-5 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-14 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-14 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-3 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-14 libstdc++6-4.4-dev_4.4.4-14 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-22 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-3 netbase_4.42 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010l-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -219,12 +223,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -239,60 +243,61 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture mips
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD is.c -o is.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD main.c -o main.o
+gcc -g -O2 -g -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-mips-rZRDcv/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -305,7 +310,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -321,6 +326,7 @@ dh_installlogcheck -pbwa
dh_installchangelogs -pbwa ./ChangeLog
dh_installudev -pbwa
dh_lintian -pbwa
+dh_bugfiles -pbwa
dh_install -pbwa
dh_link -pbwa
dh_installmime -pbwa
@@ -335,63 +341,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli at buildd.debian.org> >../bwa_0.5.8c-1_mips.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101029-1556
+Build finished at 20110211-0851
-bwa_0.5.8c-1_mips.changes:
+bwa_0.5.9-1_mips.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: mips
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- d6113de42eaf494c306e5af5f71a7237ec32f301 150432 bwa_0.5.8c-1_mips.deb
+ 9cb95ba0ae3404fcf08dbce8baa7eefa244a9ebe 156394 bwa_0.5.9-1_mips.deb
Checksums-Sha256:
- dba7aa8120e78529483a4ec3887a7e5ca2a8b5e09370a0d7f8402bdebe5e83cd 150432 bwa_0.5.8c-1_mips.deb
+ aed4284dda62177fa6e094dcf2b6f7ed2117b09eded1c1afa7fbbcaa5d480d62 156394 bwa_0.5.9-1_mips.deb
Files:
- d6c043c5d3fef29d26542a2ca36ba5a0 150432 science optional bwa_0.5.8c-1_mips.deb
+ f35b7841db06325c03b56d0d8ab231c0 156394 science optional bwa_0.5.9-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_mips.deb
-─────────────────────
+bwa_0.5.9-1_mips.deb
+────────────────────
new debian package, version 2.0.
- size 150432 bytes: control archive= 948 bytes.
- 774 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 156394 bytes: control archive= 974 bytes.
+ 773 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 360
+ Installed-Size: 372
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -405,24 +408,25 @@ bwa_0.5.8c-1_mips.deb
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 2010-10-29 15:56 ./
-drwxr-xr-x root/root 0 2010-10-29 15:56 ./usr/
-drwxr-xr-x root/root 0 2010-10-29 15:56 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-29 15:56 ./usr/share/bwa/
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
-drwxr-xr-x root/root 0 2010-10-29 15:56 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-29 15:56 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-29 15:56 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-29 15:55 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-29 15:56 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
-drwxr-xr-x root/root 0 2010-10-29 15:56 ./usr/bin/
--rwxr-xr-x root/root 243280 2010-10-29 15:56 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./usr/
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./usr/share/bwa/
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-11 08:50 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+drwxr-xr-x root/root 0 2011-02-11 08:50 ./usr/bin/
+-rwxr-xr-x root/root 254656 2011-02-11 08:50 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -431,77 +435,77 @@ drwxr-xr-x root/root 0 2010-10-29 15:56 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mips-sbuild-34058ea3-7a06-49e0-8dc2-9e8bff6ce7bc/build/buildd-bwa_0.5.8c-1-mips-AmP2Vw
+Purging /var/lib/schroot/mount/sid-mips-sbuild-dc8f20d6-132a-41bf-8c89-51f580f2ad13/build/buildd-bwa_0.5.9-1-mips-rZRDcv
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101029-1556
-Build needed 00:05:58, 2668k disc space
+Finished at 20110211-0851
+Build needed 00:06:20, 2712k disc space
-From buildd at monteverdi.ayous.org Fri Oct 29 01:15:14 2010
+From buildd at monteverdi.ayous.org Tue Feb 08 13:45:51 2011
Return-path: <buildd at monteverdi.ayous.org>
-Received: from [2001:a60:f006:deb:20a:1ff:fe00:987] (helo=monteverdi.ayous.org)
+Received: from monteverdi.ayous.org ([2001:a60:f006:deb:20a:1ff:fe00:987])
by grieg.debian.org with esmtp (Exim 4.69)
- (envelope-from <buildd at monteverdi.ayous.org>) id 1PBdYm-0002xi-GL
- for logs at buildd.debian.org; Fri, 29 Oct 2010 01:15:14 +0000
+ (envelope-from <buildd at monteverdi.ayous.org>) id 1Pmnt7-0001hr-Vu
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 13:45:50 +0000
Received: from buildd by monteverdi.ayous.org with local (Exim 4.69)
(envelope-from <buildd at monteverdi.ayous.org>)
- id 1PBdQ0-0002MF-3J; Fri, 29 Oct 2010 01:06:08 +0000
+ id 1PmnT1-0005yZ-Ga; Tue, 08 Feb 2011 13:18:51 +0000
From: buildd on monteverdi <buildd at monteverdi.ayous.org>
To: aba+buildd_monteverdi at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on mipsel (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PBdQ0-0002MF-3J at monteverdi.ayous.org>
-Date: Fri, 29 Oct 2010 01:06:08 +0000
+Message-Id: <E1PmnT1-0005yZ-Ga at monteverdi.ayous.org>
+Date: Tue, 08 Feb 2011 13:18:51 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on monteverdi.ayous.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (mipsel) 29 Oct 2010 01:01 ║
+║ bwa 0.5.9-1 (mipsel) 08 Feb 2011 13:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-801a4282-9a34-4afc-b582-ef04e5e7fc1d/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ
-Start Time: 20101029-0101
+Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-8a96403e-aef9-4007-9c02-1fefc0fbb7d8/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu
+Start Time: 20110208-1314
Get:1 http://incoming.debian.org unstable Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
Ign http://incoming.debian.org/debian/ unstable/main Translation-en
Get:2 http://incoming.debian.org Release.gpg [835 B]
-Get:3 http://mirror.ayous.org unstable Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Ign http://mirror.ayous.org/debian/ unstable/contrib Translation-en
+Get:3 http://mirror.ayous.org unstable Release.gpg [835 B]
Get:4 http://incoming.debian.org unstable Release [104 kB]
+Ign http://mirror.ayous.org/debian/ unstable/contrib Translation-en
Ign http://mirror.ayous.org/debian/ unstable/main Translation-en
Get:5 http://mirror.ayous.org unstable Release [104 kB]
-Ign http://mirror.ayous.org unstable/main Sources
-Ign http://mirror.ayous.org unstable/contrib Sources
-Ign http://mirror.ayous.org unstable/non-free Sources
-Ign http://mirror.ayous.org unstable/main mipsel Packages
-Ign http://mirror.ayous.org unstable/contrib mipsel Packages
Get:6 http://incoming.debian.org Release [1604 B]
Ign http://incoming.debian.org unstable/main Sources
Ign http://incoming.debian.org unstable/contrib Sources
Ign http://incoming.debian.org unstable/non-free Sources
Ign http://incoming.debian.org unstable/main mipsel Packages
Ign http://incoming.debian.org unstable/contrib mipsel Packages
+Ign http://mirror.ayous.org unstable/main Sources
+Ign http://mirror.ayous.org unstable/contrib Sources
+Ign http://mirror.ayous.org unstable/non-free Sources
+Ign http://mirror.ayous.org unstable/main mipsel Packages
+Ign http://mirror.ayous.org unstable/contrib mipsel Packages
+Get:7 http://incoming.debian.org unstable/main Sources [5298 kB]
+Get:8 http://mirror.ayous.org unstable/main Sources [5298 kB]
+Get:9 http://mirror.ayous.org unstable/contrib Sources [46.1 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [46.1 kB]
+Get:11 http://mirror.ayous.org unstable/non-free Sources [100 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://mirror.ayous.org unstable/main mipsel Packages [8929 kB]
+Get:14 http://incoming.debian.org unstable/main mipsel Packages [8929 kB]
+Get:15 http://mirror.ayous.org unstable/contrib mipsel Packages [61.3 kB]
+Get:16 http://incoming.debian.org unstable/contrib mipsel Packages [61.3 kB]
Ign http://incoming.debian.org Sources
Ign http://incoming.debian.org Packages
-Get:7 http://mirror.ayous.org unstable/main Sources [5166 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [5166 kB]
-Get:9 http://mirror.ayous.org unstable/contrib Sources [46.1 kB]
-Get:10 http://mirror.ayous.org unstable/non-free Sources [97.3 kB]
-Get:11 http://mirror.ayous.org unstable/main mipsel Packages [8768 kB]
-Get:12 http://incoming.debian.org unstable/contrib Sources [46.1 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [97.3 kB]
-Get:14 http://incoming.debian.org unstable/main mipsel Packages [8768 kB]
-Get:15 http://mirror.ayous.org unstable/contrib mipsel Packages [62.2 kB]
-Get:16 http://incoming.debian.org unstable/contrib mipsel Packages [62.2 kB]
-Get:17 http://incoming.debian.org Sources [19.9 kB]
-Get:18 http://incoming.debian.org Packages [249 kB]
-Fetched 28.8 MB in 30s (944 kB/s)
+Get:17 http://incoming.debian.org Sources [60.0 kB]
+Get:18 http://incoming.debian.org Packages [1020 kB]
+Fetched 30.2 MB in 51s (588 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -520,20 +524,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120 kB of source archives.
-Get:1 http://mirror.ayous.org/debian/ unstable/main bwa 0.5.8c-1 (dsc) [1905 B]
-Get:2 http://mirror.ayous.org/debian/ unstable/main bwa 0.5.8c-1 (tar) [114 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main bwa 0.5.8c-1 (diff) [4005 B]
-Fetched 120 kB in 1s (119 kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 2s (53.5 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -542,7 +546,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -563,36 +567,36 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 15 not upgraded.
-Need to get 9971 kB of archives.
-After this operation, 30.1 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.0.13 [205 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.20.1-10 [1188 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.7-6 [1247 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.02-1.1 [233 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.7.dfsg-4 [832 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.24.2-1 [1039 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16 [224 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
+0 upgraded, 18 newly installed, 0 to remove and 60 not upgraded.
+Need to get 10.1 MB of archives.
+After this operation, 30.5 MB of additional disk space will be used.
+Get:1 http://incoming.debian.org/buildd-unstable/ cdbs 0.4.92 [1268 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.2 [207 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.20.1-10 [1188 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.7-8 [1248 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.02-1.1 [233 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-2 [833 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.24.2-1 [1039 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.1.0 [552 kB]
Get:18 http://mirror.ayous.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 9971 kB in 2s (4407 kB/s)
+Fetched 10.1 MB in 2s (4869 kB/s)
Selecting previously deselected package bsdmainutils.
(Reading database ... 10134 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_mipsel.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mipsel.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_mipsel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_mipsel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_mipsel.deb) ...
Selecting previously deselected package file.
@@ -602,7 +606,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mipsel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_mipsel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -616,39 +620,39 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
-Setting up cdbs (0.4.89) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
+Setting up cdbs (0.4.92) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.33-rc7 mipsel (mips64)
Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.5-2 g++-4.4_4.4.5-2 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-2 libstdc++6_4.4.5-2
-Package versions: apt_0.8.6 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.6 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.2.2 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -660,12 +664,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -680,60 +684,61 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture mipsel
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD is.c -o is.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD main.c -o main.o
+gcc -g -O2 -g -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -746,7 +751,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -762,6 +767,7 @@ dh_installlogcheck -pbwa
dh_installchangelogs -pbwa ./ChangeLog
dh_installudev -pbwa
dh_lintian -pbwa
+dh_bugfiles -pbwa
dh_install -pbwa
dh_link -pbwa
dh_installmime -pbwa
@@ -776,63 +782,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org> >../bwa_0.5.8c-1_mipsel.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101029-0106
+Build finished at 20110208-1318
-bwa_0.5.8c-1_mipsel.changes:
+bwa_0.5.9-1_mipsel.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: mipsel
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- e39c527f667cb7ca5b829061bb25984a49326822 151368 bwa_0.5.8c-1_mipsel.deb
+ 83efb08fe3f4c356780afb66bb8aca68f78600d5 157276 bwa_0.5.9-1_mipsel.deb
Checksums-Sha256:
- 6548cd13422f5d947fdef97a96f92e91cbcf6bdc0644a088febfbc4072264906 151368 bwa_0.5.8c-1_mipsel.deb
+ c7669f6291a12ab71bc129dc270a68628eda67602a4128e517f13d3b22984036 157276 bwa_0.5.9-1_mipsel.deb
Files:
- fbed2e137bb9753c0eaa6428df106863 151368 science optional bwa_0.5.8c-1_mipsel.deb
+ 4fe2161fb763a828f545819c8c39e7fa 157276 science optional bwa_0.5.9-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_mipsel.deb
-───────────────────────
+bwa_0.5.9-1_mipsel.deb
+──────────────────────
new debian package, version 2.0.
- size 151368 bytes: control archive= 946 bytes.
- 776 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 157276 bytes: control archive= 977 bytes.
+ 775 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 360
+ Installed-Size: 372
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -846,24 +849,25 @@ bwa_0.5.8c-1_mipsel.deb
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 2010-10-29 01:05 ./
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-29 01:05 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/bin/
--rwxr-xr-x root/root 244208 2010-10-29 01:05 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 13:18 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/bin/
+-rwxr-xr-x root/root 254656 2011-02-08 13:18 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -872,9 +876,9 @@ drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-801a4282-9a34-4afc-b582-ef04e5e7fc1d/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-8a96403e-aef9-4007-9c02-1fefc0fbb7d8/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101029-0106
-Build needed 00:04:18, 2668k disc space
+Finished at 20110208-1318
+Build needed 00:04:43, 2712k disc space
diff --git a/mipsel.log b/mipsel.log
index b1eab79..6243e51 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,68 +1,68 @@
-From buildd at monteverdi.ayous.org Fri Oct 29 01:15:14 2010
+From buildd at monteverdi.ayous.org Tue Feb 08 13:45:51 2011
Return-path: <buildd at monteverdi.ayous.org>
-Received: from [2001:a60:f006:deb:20a:1ff:fe00:987] (helo=monteverdi.ayous.org)
+Received: from monteverdi.ayous.org ([2001:a60:f006:deb:20a:1ff:fe00:987])
by grieg.debian.org with esmtp (Exim 4.69)
- (envelope-from <buildd at monteverdi.ayous.org>) id 1PBdYm-0002xi-GL
- for logs at buildd.debian.org; Fri, 29 Oct 2010 01:15:14 +0000
+ (envelope-from <buildd at monteverdi.ayous.org>) id 1Pmnt7-0001hr-Vu
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 13:45:50 +0000
Received: from buildd by monteverdi.ayous.org with local (Exim 4.69)
(envelope-from <buildd at monteverdi.ayous.org>)
- id 1PBdQ0-0002MF-3J; Fri, 29 Oct 2010 01:06:08 +0000
+ id 1PmnT1-0005yZ-Ga; Tue, 08 Feb 2011 13:18:51 +0000
From: buildd on monteverdi <buildd at monteverdi.ayous.org>
To: aba+buildd_monteverdi at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on mipsel (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PBdQ0-0002MF-3J at monteverdi.ayous.org>
-Date: Fri, 29 Oct 2010 01:06:08 +0000
+Message-Id: <E1PmnT1-0005yZ-Ga at monteverdi.ayous.org>
+Date: Tue, 08 Feb 2011 13:18:51 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on monteverdi.ayous.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (mipsel) 29 Oct 2010 01:01 ║
+║ bwa 0.5.9-1 (mipsel) 08 Feb 2011 13:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-801a4282-9a34-4afc-b582-ef04e5e7fc1d/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ
-Start Time: 20101029-0101
+Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-8a96403e-aef9-4007-9c02-1fefc0fbb7d8/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu
+Start Time: 20110208-1314
Get:1 http://incoming.debian.org unstable Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
Ign http://incoming.debian.org/debian/ unstable/main Translation-en
Get:2 http://incoming.debian.org Release.gpg [835 B]
-Get:3 http://mirror.ayous.org unstable Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Ign http://mirror.ayous.org/debian/ unstable/contrib Translation-en
+Get:3 http://mirror.ayous.org unstable Release.gpg [835 B]
Get:4 http://incoming.debian.org unstable Release [104 kB]
+Ign http://mirror.ayous.org/debian/ unstable/contrib Translation-en
Ign http://mirror.ayous.org/debian/ unstable/main Translation-en
Get:5 http://mirror.ayous.org unstable Release [104 kB]
-Ign http://mirror.ayous.org unstable/main Sources
-Ign http://mirror.ayous.org unstable/contrib Sources
-Ign http://mirror.ayous.org unstable/non-free Sources
-Ign http://mirror.ayous.org unstable/main mipsel Packages
-Ign http://mirror.ayous.org unstable/contrib mipsel Packages
Get:6 http://incoming.debian.org Release [1604 B]
Ign http://incoming.debian.org unstable/main Sources
Ign http://incoming.debian.org unstable/contrib Sources
Ign http://incoming.debian.org unstable/non-free Sources
Ign http://incoming.debian.org unstable/main mipsel Packages
Ign http://incoming.debian.org unstable/contrib mipsel Packages
+Ign http://mirror.ayous.org unstable/main Sources
+Ign http://mirror.ayous.org unstable/contrib Sources
+Ign http://mirror.ayous.org unstable/non-free Sources
+Ign http://mirror.ayous.org unstable/main mipsel Packages
+Ign http://mirror.ayous.org unstable/contrib mipsel Packages
+Get:7 http://incoming.debian.org unstable/main Sources [5298 kB]
+Get:8 http://mirror.ayous.org unstable/main Sources [5298 kB]
+Get:9 http://mirror.ayous.org unstable/contrib Sources [46.1 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [46.1 kB]
+Get:11 http://mirror.ayous.org unstable/non-free Sources [100 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://mirror.ayous.org unstable/main mipsel Packages [8929 kB]
+Get:14 http://incoming.debian.org unstable/main mipsel Packages [8929 kB]
+Get:15 http://mirror.ayous.org unstable/contrib mipsel Packages [61.3 kB]
+Get:16 http://incoming.debian.org unstable/contrib mipsel Packages [61.3 kB]
Ign http://incoming.debian.org Sources
Ign http://incoming.debian.org Packages
-Get:7 http://mirror.ayous.org unstable/main Sources [5166 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [5166 kB]
-Get:9 http://mirror.ayous.org unstable/contrib Sources [46.1 kB]
-Get:10 http://mirror.ayous.org unstable/non-free Sources [97.3 kB]
-Get:11 http://mirror.ayous.org unstable/main mipsel Packages [8768 kB]
-Get:12 http://incoming.debian.org unstable/contrib Sources [46.1 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [97.3 kB]
-Get:14 http://incoming.debian.org unstable/main mipsel Packages [8768 kB]
-Get:15 http://mirror.ayous.org unstable/contrib mipsel Packages [62.2 kB]
-Get:16 http://incoming.debian.org unstable/contrib mipsel Packages [62.2 kB]
-Get:17 http://incoming.debian.org Sources [19.9 kB]
-Get:18 http://incoming.debian.org Packages [249 kB]
-Fetched 28.8 MB in 30s (944 kB/s)
+Get:17 http://incoming.debian.org Sources [60.0 kB]
+Get:18 http://incoming.debian.org Packages [1020 kB]
+Fetched 30.2 MB in 51s (588 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -81,20 +81,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120 kB of source archives.
-Get:1 http://mirror.ayous.org/debian/ unstable/main bwa 0.5.8c-1 (dsc) [1905 B]
-Get:2 http://mirror.ayous.org/debian/ unstable/main bwa 0.5.8c-1 (tar) [114 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main bwa 0.5.8c-1 (diff) [4005 B]
-Fetched 120 kB in 1s (119 kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 2s (53.5 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -103,7 +103,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -124,36 +124,36 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 15 not upgraded.
-Need to get 9971 kB of archives.
-After this operation, 30.1 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.0.13 [205 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.20.1-10 [1188 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.7-6 [1247 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.02-1.1 [233 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.7.dfsg-4 [832 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.24.2-1 [1039 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16 [224 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
+0 upgraded, 18 newly installed, 0 to remove and 60 not upgraded.
+Need to get 10.1 MB of archives.
+After this operation, 30.5 MB of additional disk space will be used.
+Get:1 http://incoming.debian.org/buildd-unstable/ cdbs 0.4.92 [1268 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.2 [207 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.20.1-10 [1188 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.7-8 [1248 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.02-1.1 [233 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-2 [833 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.24.2-1 [1039 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.1.0 [552 kB]
Get:18 http://mirror.ayous.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 9971 kB in 2s (4407 kB/s)
+Fetched 10.1 MB in 2s (4869 kB/s)
Selecting previously deselected package bsdmainutils.
(Reading database ... 10134 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_mipsel.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mipsel.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_mipsel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_mipsel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_mipsel.deb) ...
Selecting previously deselected package file.
@@ -163,7 +163,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mipsel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_mipsel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -177,39 +177,39 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
-Setting up cdbs (0.4.89) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
+Setting up cdbs (0.4.92) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.33-rc7 mipsel (mips64)
Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.5-2 g++-4.4_4.4.5-2 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-2 libstdc++6_4.4.5-2
-Package versions: apt_0.8.6 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.6 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.2.2 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -221,12 +221,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -241,60 +241,61 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture mipsel
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD is.c -o is.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD main.c -o main.o
+gcc -g -O2 -g -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -307,7 +308,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -323,6 +324,7 @@ dh_installlogcheck -pbwa
dh_installchangelogs -pbwa ./ChangeLog
dh_installudev -pbwa
dh_lintian -pbwa
+dh_bugfiles -pbwa
dh_install -pbwa
dh_link -pbwa
dh_installmime -pbwa
@@ -337,63 +339,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org> >../bwa_0.5.8c-1_mipsel.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101029-0106
+Build finished at 20110208-1318
-bwa_0.5.8c-1_mipsel.changes:
+bwa_0.5.9-1_mipsel.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: mipsel
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- e39c527f667cb7ca5b829061bb25984a49326822 151368 bwa_0.5.8c-1_mipsel.deb
+ 83efb08fe3f4c356780afb66bb8aca68f78600d5 157276 bwa_0.5.9-1_mipsel.deb
Checksums-Sha256:
- 6548cd13422f5d947fdef97a96f92e91cbcf6bdc0644a088febfbc4072264906 151368 bwa_0.5.8c-1_mipsel.deb
+ c7669f6291a12ab71bc129dc270a68628eda67602a4128e517f13d3b22984036 157276 bwa_0.5.9-1_mipsel.deb
Files:
- fbed2e137bb9753c0eaa6428df106863 151368 science optional bwa_0.5.8c-1_mipsel.deb
+ 4fe2161fb763a828f545819c8c39e7fa 157276 science optional bwa_0.5.9-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_mipsel.deb
-───────────────────────
+bwa_0.5.9-1_mipsel.deb
+──────────────────────
new debian package, version 2.0.
- size 151368 bytes: control archive= 946 bytes.
- 776 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 157276 bytes: control archive= 977 bytes.
+ 775 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 360
+ Installed-Size: 372
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -407,24 +406,25 @@ bwa_0.5.8c-1_mipsel.deb
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 2010-10-29 01:05 ./
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-29 01:05 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/bin/
--rwxr-xr-x root/root 244208 2010-10-29 01:05 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 13:18 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 13:18 ./usr/bin/
+-rwxr-xr-x root/root 254656 2011-02-08 13:18 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -433,9 +433,9 @@ drwxr-xr-x root/root 0 2010-10-29 01:05 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-801a4282-9a34-4afc-b582-ef04e5e7fc1d/build/buildd-bwa_0.5.8c-1-mipsel-Kl06bQ
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-8a96403e-aef9-4007-9c02-1fefc0fbb7d8/build/buildd-bwa_0.5.9-1-mipsel-9vjpUu
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101029-0106
-Build needed 00:04:18, 2668k disc space
+Finished at 20110208-1318
+Build needed 00:04:43, 2712k disc space
diff --git a/powerpc.log b/powerpc.log
index 28d2480..d8ba34b 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,67 +1,96 @@
-From buildd at poulenc.debian.org Wed Oct 27 12:38:50 2010
-Return-path: <buildd at poulenc.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd at voltaire.debian.org Tue Feb 08 09:03:56 2011
+Return-path: <buildd at voltaire.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 4.69) (envelope-from <buildd at poulenc.debian.org>)
- id 1PB5HG-0004gk-MM
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:38:50 +0000
-Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
- helo=poulenc.debian.org)
+ (Exim 4.69) (envelope-from <buildd at voltaire.debian.org>)
+ id 1PmjUK-0004Dh-77
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 09:03:56 +0000
+Received: from static-72-66-115-54.washdc.fios.verizon.net ([72.66.115.54]
+ helo=voltaire.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=poulenc.debian.org, EMAIL=hostmaster at poulenc.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at poulenc.debian.org>)
- id 1PB5HB-0004Yi-KB; Wed, 27 Oct 2010 12:38:49 +0000
-Received: from buildd by poulenc.debian.org with local (Exim 4.69)
- (envelope-from <buildd at poulenc.debian.org>)
- id 1PB5H8-0001gf-V9; Wed, 27 Oct 2010 12:38:42 +0000
-From: buildd on poulenc <buildd at poulenc.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on powerpc (dist=unstable)
+ CN=voltaire.debian.org,
+ EMAIL=hostmaster at voltaire.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at voltaire.debian.org>)
+ id 1PmjUI-0002SJ-NG; Tue, 08 Feb 2011 09:03:55 +0000
+Received: from buildd by voltaire.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at voltaire.debian.org>)
+ id 1PmjUB-00069N-Fb; Tue, 08 Feb 2011 09:03:47 +0000
+From: buildd on voltaire <buildd at voltaire.debian.org>
+To: wouter+buildd at grep.be,logs at buildd.debian.org
+Subject: Log for successful build of bwa_0.5.9-1 on powerpc (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PB5H8-0001gf-V9 at poulenc.debian.org>
-Date: Wed, 27 Oct 2010 12:38:42 +0000
+Message-Id: <E1PmjUB-00069N-Fb at voltaire.debian.org>
+Date: Tue, 08 Feb 2011 09:03:47 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on poulenc.debian.org
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on voltaire.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (powerpc) 27 Oct 2010 12:37 ║
+║ bwa 0.5.9-1 (powerpc) 08 Feb 2011 09:00 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: powerpc
-Chroot Build Dir: /var/lib/schroot/mount/sid-powerpc-sbuild-8911e019-c490-4812-a9c8-09eb38c43db9/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp
-Start Time: 20101027-1237
-Get:1 http://ftp.uk.debian.org unstable Release.gpg [835B]
-Ign http://ftp.uk.debian.org/debian/ unstable/contrib Translation-en
-Ign http://ftp.uk.debian.org/debian/ unstable/main Translation-en
-Get:2 http://ftp.uk.debian.org unstable Release [104kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [4008kB]
-Get:4 http://incoming.debian.org unstable Release.gpg [835B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:5 http://incoming.debian.org Release.gpg [835B]
+Chroot Build Dir: /var/lib/schroot/mount/sid-powerpc-sbuild-2c45f9c7-7419-4779-bb11-9d254b562d98/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn
+Start Time: 20110208-0900
+Get:1 http://incoming.debian.org sid Release.gpg [835 B]
+Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
+Ign http://incoming.debian.org/debian/ sid/main Translation-en
+Get:2 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:6 http://incoming.debian.org unstable Release [104kB]
-Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4008kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib Sources [38.7kB]
-Get:10 http://ftp.uk.debian.org unstable/non-free Sources [80.3kB]
-Get:11 http://ftp.uk.debian.org unstable/main powerpc Packages [6772kB]
-Get:12 http://ftp.uk.debian.org unstable/contrib powerpc Packages [50.1kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [80.3kB]
-Get:15 http://incoming.debian.org unstable/main powerpc Packages [6772kB]
-Get:16 http://incoming.debian.org unstable/contrib powerpc Packages [50.1kB]
-Get:17 http://incoming.debian.org Sources [23.4kB]
-Get:18 http://incoming.debian.org Packages [85.4kB]
-Fetched 22.2MB in 24s (906kB/s)
+Get:3 http://incoming.debian.org sid Release [104 kB]
+Get:4 http://incoming.debian.org Release [1604 B]
+Get:5 http://http.us.debian.org sid Release.gpg [835 B]
+Ign http://http.us.debian.org/debian/ sid/contrib Translation-en
+Ign http://http.us.debian.org/debian/ sid/main Translation-en
+Get:6 http://http.us.debian.org sid Release [104 kB]
+Get:7 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:8 http://incoming.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:9 http://incoming.debian.org sid/main powerpc Packages/DiffIndex [2038 B]
+Get:10 http://incoming.debian.org sid/contrib powerpc Packages/DiffIndex [2023 B]
+Get:11 http://incoming.debian.org Sources [43.1 kB]
+Get:12 http://http.us.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:13 http://incoming.debian.org Packages [680 kB]
+Get:14 http://incoming.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:15 http://incoming.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:16 http://incoming.debian.org sid/main powerpc 2011-02-08-0211.24.pdiff [5220 B]
+Get:17 http://incoming.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:18 http://incoming.debian.org sid/contrib powerpc 2011-02-08-0211.24.pdiff [301 B]
+Get:19 http://http.us.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:20 http://http.us.debian.org sid/main powerpc Packages/DiffIndex [2038 B]
+Get:21 http://http.us.debian.org sid/contrib powerpc Packages/DiffIndex [2023 B]
+Get:22 http://incoming.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:23 http://incoming.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:24 http://http.us.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:25 http://http.us.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:26 http://incoming.debian.org sid/main powerpc 2011-02-08-0211.24.pdiff [5220 B]
+Get:27 http://incoming.debian.org sid/contrib powerpc 2011-02-08-0211.24.pdiff [301 B]
+Get:28 http://http.us.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:29 http://http.us.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:30 http://http.us.debian.org sid/main powerpc 2011-02-08-0211.24.pdiff [5220 B]
+Get:31 http://http.us.debian.org sid/main powerpc 2011-02-08-0211.24.pdiff [5220 B]
+Get:32 http://http.us.debian.org sid/contrib powerpc 2011-02-08-0211.24.pdiff [301 B]
+Get:33 http://http.us.debian.org sid/contrib powerpc 2011-02-08-0211.24.pdiff [301 B]
+Get:34 http://incoming.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:35 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:36 http://incoming.debian.org sid/main powerpc 2011-02-08-0211.24.pdiff [5220 B]
+Get:37 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:38 http://incoming.debian.org sid/contrib powerpc 2011-02-08-0211.24.pdiff [301 B]
+Get:39 http://http.us.debian.org sid/main 2011-02-08-0211.24.pdiff [13.5 kB]
+Get:40 http://incoming.debian.org sid/main powerpc 2011-02-08-0812.10.pdiff [1594 B]
+Get:41 http://incoming.debian.org sid/main powerpc 2011-02-08-0812.10.pdiff [1594 B]
+Get:42 http://http.us.debian.org sid/contrib 2011-02-08-0211.24.pdiff [266 B]
+Get:43 http://http.us.debian.org sid/main powerpc 2011-02-08-0211.24.pdiff [5220 B]
+Get:44 http://http.us.debian.org sid/contrib powerpc 2011-02-08-0211.24.pdiff [301 B]
+Get:45 http://incoming.debian.org sid/main 2011-02-08-0812.10.pdiff [3472 B]
+Get:46 http://incoming.debian.org sid/main powerpc 2011-02-08-0812.10.pdiff [1594 B]
+Fetched 994 kB in 45s (21.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,20 +109,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-NOTICE: 'bwa' packaging is maintained in the 'Svn' version control system at:
-svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 0s (146kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 0s (572 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -101,114 +130,36 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
-debhelper: missing
-Using default version 8.0.0
+debhelper: already installed (8.1.0 >= 8 is satisfied)
zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies: cdbs debhelper zlib1g-dev
+Installing positive dependencies: cdbs zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
- po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ devscripts doc-base
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
- libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 34 not upgraded.
-Need to get 10.1MB of archives.
-After this operation, 29.3MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.0.13 [205kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.20.1-10 [1196kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.5.7-6 [1285kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5 [241kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5 [49.9kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-3 [141kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.02-1.1 [231kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.7.dfsg-4 [848kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.24.2-1 [1111kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-3 [422kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16 [224kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190kB]
+ cdbs zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.1MB in 1s (5128kB/s)
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10125 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_powerpc.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_powerpc.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_powerpc.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_powerpc.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5_powerpc.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpc.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_powerpc.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_powerpc.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_powerpc.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_powerpc.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_powerpc.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+0 upgraded, 2 newly installed, 0 to remove and 1 not upgraded.
+Need to get 0 B/1431 kB of archives.
+After this operation, 2122 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
+(Reading database ... 14253 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
-Setting up bsdmainutils (8.0.13) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Processing triggers for man-db ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-Kernel: Linux 2.6.26-2-powerpc64 powerpc (ppc64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.4-17 g++-4.4_4.4.4-17 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-17 libstdc++6_4.4.4-17
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-17 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-17 gcc_4:4.4.4-2 gcc-4.4_4.4.4-17 gcc-4.4-base_4.4.4-17 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-17 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-17 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-3 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-17 libstdc++6-4.4-dev_4.4.4-17 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-24 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-3 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-3 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.26-2-powerpc-smp powerpc (ppc)
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: adduser_3.112+nmu2 apt_0.8.10.3 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-6 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 ifupdown_0.6.10 initscripts_2.88dsf-13.1 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libalgorithm-diff-perl_1.19.02-2 libalgorithm-merge-perl_0.08-2 libattr1_1:2.4.44-2 libblkid1_2.17.2-9 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-10 libgpg-error0_1.6-1 libgpm2_1.20.4-3.3 libldap-2.4-2_2.4.23-7 liblzma2_5.0.0-2 liblzo2-2_2.03-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncursesw5_5.7+20100313-5 libnewt0.52_0.52.11-2 libopencdk10_0.6.6-1 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libssl0.9.8_0.9.8o-4 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.7-8 manpages_3.27-1 manpages-dev_3.27-1 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 net-tools_1.60-23 netbase_4.45 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.71-4 sudo_1.7.4p4-6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011a-1 util-linux_2.17.2-9 whiptail_0.52.11-2 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -220,12 +171,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -240,36 +191,37 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+dpkg: warning: failed to open configuration file '/home/buildd/.dpkg.cfg' for reading: Permission denied
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture powerpc
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c'
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9/bwt_gen'
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
@@ -291,9 +243,10 @@ gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp/bwa-0.5.8c'
+gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -306,7 +259,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -336,63 +289,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../bwa_0.5.8c-1_powerpc.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (voltaire) <buildd_powerpc-voltaire at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1238
+Build finished at 20110208-0903
-bwa_0.5.8c-1_powerpc.changes:
+bwa_0.5.9-1_powerpc.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: powerpc
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
+Maintainer: powerpc Build Daemon (voltaire) <buildd_powerpc-voltaire at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- e4ea7d6eda7616f394ea9b9c0f46978d38577ed0 146830 bwa_0.5.8c-1_powerpc.deb
+ cc78264519720b5ecc586c1b3c7c1a1533e28613 152162 bwa_0.5.9-1_powerpc.deb
Checksums-Sha256:
- 599937aa6d14312267fd60bfd249f197870ca149ceac65a3a40dca7cb344f904 146830 bwa_0.5.8c-1_powerpc.deb
+ b8f6c704282dfa477e1c0cd0e7fd7986c65c11838b077c6bbcbf3c79e96830f3 152162 bwa_0.5.9-1_powerpc.deb
Files:
- 37f2fa18b7c914862cf86167dc221618 146830 science optional bwa_0.5.8c-1_powerpc.deb
+ 6f2d8fcaa662eb9287b54e6d68498267 152162 science optional bwa_0.5.9-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_powerpc.deb
-────────────────────────
+bwa_0.5.9-1_powerpc.deb
+───────────────────────
new debian package, version 2.0.
- size 146830 bytes: control archive= 947 bytes.
- 777 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 152162 bytes: control archive= 973 bytes.
+ 776 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 336
+ Installed-Size: 344
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -406,24 +356,25 @@ bwa_0.5.8c-1_powerpc.deb
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 2010-10-27 12:38 ./
-drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:38 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
-drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/bin/
--rwxr-xr-x root/root 218912 2010-10-27 12:38 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 09:03 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 09:03 ./usr/bin/
+-rwxr-xr-x root/root 227172 2011-02-08 09:03 ./usr/bin/bwa
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -432,9 +383,12 @@ drwxr-xr-x root/root 0 2010-10-27 12:38 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-8911e019-c490-4812-a9c8-09eb38c43db9/build/buildd-bwa_0.5.8c-1-powerpc-hR0qqp
-Not removing build depends: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-2c45f9c7-7419-4779-bb11-9d254b562d98/build/buildd-bwa_0.5.9-1-powerpc-A4NKHn
+(Reading database ... 14333 files and directories currently installed.)
+Removing cdbs ...
+Removing zlib1g-dev ...
+Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1238
-Build needed 00:01:31, 2628k disc space
+Finished at 20110208-0903
+Build needed 00:03:30, 2656k disc space
diff --git a/s390.log b/s390.log
index d6d23a6..1ba5d44 100644
--- a/s390.log
+++ b/s390.log
@@ -1,4 +1,4 @@
-From buildd at zandonai.debian.org Wed Oct 27 12:41:40 2010
+From buildd at zandonai.debian.org Tue Feb 08 20:35:27 2011
Return-path: <buildd at zandonai.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,
@@ -6,58 +6,65 @@ 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 4.69) (envelope-from <buildd at zandonai.debian.org>)
- id 1PB5Jz-000527-O1
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:41:40 +0000
+ id 1PmuHX-00019w-Hl
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 20:35:27 +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 merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at zandonai.debian.org>)
- id 1PB5Jy-00075m-D5; Wed, 27 Oct 2010 12:41:38 +0000
+ id 1PmuHW-0003pl-6q; Tue, 08 Feb 2011 20:35:26 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.69)
(envelope-from <buildd at zandonai.debian.org>)
- id 1PB5Jx-0006tT-Fe; Wed, 27 Oct 2010 12:41:37 +0000
+ id 1PmuHV-0006Z7-LC; Tue, 08 Feb 2011 20:35:25 +0000
From: buildd on zandonai <buildd at zandonai.debian.org>
-To: aba at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.8c-1 on s390 (dist=unstable)
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of bwa_0.5.9-1 on s390 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PB5Jx-0006tT-Fe at zandonai.debian.org>
-Date: Wed, 27 Oct 2010 12:41:37 +0000
+Message-Id: <E1PmuHV-0006Z7-LC at zandonai.debian.org>
+Date: Tue, 08 Feb 2011 20:35:25 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (s390) 27 Oct 2010 12:40 ║
+║ bwa 0.5.9-1 (s390) 08 Feb 2011 20:34 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: s390
-Chroot Build Dir: /var/lib/schroot/mount/sid-s390-sbuild-97f0cde4-7fba-4981-b6d9-f8e39bfd0fde/build/buildd-bwa_0.5.8c-1-s390-OQZpl7
-Start Time: 20101027-1240
-Get:1 http://ftp.de.debian.org unstable Release.gpg [835B]
-Get:2 http://ftp.de.debian.org unstable Release [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
-Get:4 http://incoming.debian.org Release.gpg [835B]
-Get:5 http://incoming.debian.org unstable Release [104kB]
-Get:6 http://ftp.de.debian.org unstable/main Packages [6679kB]
-Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Packages [6679kB]
-Get:9 http://ftp.de.debian.org unstable/contrib Packages [48.9kB]
-Get:10 http://ftp.de.debian.org unstable/main Sources [4008kB]
-Get:11 http://ftp.de.debian.org unstable/contrib Sources [38.7kB]
-Get:12 http://ftp.de.debian.org unstable/non-free Sources [80.3kB]
-Get:13 http://incoming.debian.org unstable/contrib Packages [48.9kB]
-Get:14 http://incoming.debian.org unstable/main Sources [4008kB]
-Get:15 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:16 http://incoming.debian.org unstable/non-free Sources [80.3kB]
-Get:17 http://incoming.debian.org Packages [85.4kB]
-Get:18 http://incoming.debian.org Sources [23.4kB]
-Fetched 22.0MB in 23s (921kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/sid-s390-sbuild-7b7874c9-18b1-486f-8396-68c0f241110c/build/buildd-bwa_0.5.9-1-s390-AOoRjJ
+Start Time: 20110208-2034
+Get:1 http://ftp.de.debian.org unstable Release.gpg [835 B]
+Ign http://ftp.de.debian.org/debian/ unstable/contrib Translation-en
+Ign http://ftp.de.debian.org/debian/ unstable/main Translation-en
+Get:2 http://ftp.de.debian.org unstable Release [104 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [4124 kB]
+Get:4 http://incoming.debian.org unstable Release.gpg [835 B]
+Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
+Ign http://incoming.debian.org/debian/ unstable/main Translation-en
+Get:5 http://incoming.debian.org Release.gpg [835 B]
+Ign http://incoming.debian.org/buildd-unstable/ Translation-en
+Get:6 http://incoming.debian.org unstable Release [104 kB]
+Get:7 http://incoming.debian.org Release [1604 B]
+Ign http://incoming.debian.org unstable Release
+Get:8 http://incoming.debian.org unstable/main Sources [4124 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib Sources [38.6 kB]
+Get:10 http://ftp.de.debian.org unstable/non-free Sources [84.3 kB]
+Get:11 http://ftp.de.debian.org unstable/main s390 Packages [6796 kB]
+Get:12 http://ftp.de.debian.org unstable/contrib s390 Packages [49.3 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [38.6 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [84.3 kB]
+Get:15 http://incoming.debian.org unstable/main s390 Packages [6796 kB]
+Get:16 http://incoming.debian.org unstable/contrib s390 Packages [49.3 kB]
+Get:17 http://incoming.debian.org Sources [41.1 kB]
+Get:18 http://incoming.debian.org Packages [571 kB]
+Fetched 23.0 MB in 32s (713 kB/s)
Reading package lists...
+W: GPG error: http://incoming.debian.org unstable Release: The following signatures were invalid: BADSIG 9AA38DCD55BE302B Debian Archive Automatic Signing Key (5.0/lenny) <ftpmaster at debian.org>
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -75,18 +82,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 0s (133kB/s)
+NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bwa.git
+Need to get 119 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main bwa 0.5.9-1 (dsc) [1894 B]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main bwa 0.5.9-1 (tar) [114 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main bwa 0.5.9-1 (diff) [3651 B]
+Fetched 119 kB in 0s (771 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -95,7 +104,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -116,36 +125,36 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 63 not upgraded.
-Need to get 10.2MB of archives.
-After this operation, 28.8MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org unstable/main bsdmainutils 8.0.13 [206kB]
-Get:2 http://ftp.de.debian.org unstable/main groff-base 1.20.1-10 [1112kB]
-Get:3 http://ftp.de.debian.org unstable/main man-db 2.5.7-6 [1308kB]
-Get:4 http://ftp.de.debian.org unstable/main libmagic1 5.04-5 [243kB]
-Get:5 http://ftp.de.debian.org unstable/main file 5.04-5 [50.0kB]
-Get:6 http://ftp.de.debian.org unstable/main gettext-base 0.18.1.1-3 [142kB]
-Get:7 http://ftp.de.debian.org unstable/main libpcre3 8.02-1.1 [239kB]
-Get:8 http://ftp.de.debian.org unstable/main libxml2 2.7.7.dfsg-4 [872kB]
-Get:9 http://ftp.de.debian.org unstable/main html2text 1.3.2a-15 [101kB]
-Get:10 http://ftp.de.debian.org unstable/main libglib2.0-0 2.24.2-1 [1140kB]
-Get:11 http://ftp.de.debian.org unstable/main libcroco3 0.6.2-1 [128kB]
-Get:12 http://ftp.de.debian.org unstable/main libunistring0 0.9.3-3 [431kB]
-Get:13 http://ftp.de.debian.org unstable/main gettext 0.18.1.1-3 [2068kB]
-Get:14 http://ftp.de.debian.org unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
-Get:15 http://ftp.de.debian.org unstable/main po-debconf 1.0.16 [224kB]
-Get:16 http://ftp.de.debian.org unstable/main debhelper 8.0.0 [454kB]
-Get:17 http://ftp.de.debian.org unstable/main cdbs 0.4.89 [1240kB]
-Get:18 http://ftp.de.debian.org unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [193kB]
+0 upgraded, 18 newly installed, 0 to remove and 23 not upgraded.
+Need to get 10.3 MB of archives.
+After this operation, 29.2 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.2 [208 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.20.1-10 [1112 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ libpcre3 8.12-1 [262 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.5.7-8 [1303 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2 [873 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.24.2-1 [1140 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-3 [431 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.1.0 [552 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:18 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 10.2MB in 3s (3102kB/s)
+Fetched 10.3 MB in 2s (3566 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10050 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_s390.deb) ...
+(Reading database ... 10088 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_s390.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_s390.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_s390.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_s390.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_s390.deb) ...
Selecting previously deselected package file.
@@ -153,9 +162,9 @@ Unpacking file (from .../archives/file_5.04-5_s390.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_s390.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_s390.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-1_s390.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_s390.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_s390.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -169,39 +178,39 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_s390.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libpcre3 (8.12-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
-Setting up cdbs (0.4.89) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
+Setting up cdbs (0.4.92) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-bpo.5-s390x s390 (s390x)
-Toolchain package versions: libc6-dev_2.11.2-2 dpkg-dev_1.15.8.3 linux-libc-dev_2.6.32-20 gcc-4.4_4.4.4-8 g++-4.4_4.4.4-8 binutils_2.20.1-13 libstdc++6-4.4-dev_4.4.4-8 libstdc++6_4.4.4-8
-Package versions: apt_0.7.25.3 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-13 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-4 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-8 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.4 diffutils_1:3.0-1 dmsetup_2:1.02.48-2 dpkg_1.15.8.3 dpkg-dev_1.15.8.3 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-8 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.4-2 gcc-4.4_4.4.4-8 gcc-4.4-base_4.4.4-8 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-4 libc-bin_2.11.2-2 libc-dev-bin_2.11.2-2 libc6_2.11.2-2 libc6-dev_2.11.2-2 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-1 libdevmapper1.02.1_2:1.02.48-2 libdpkg-perl_1.15.8.3 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-8 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100713-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-2 libncursesw5_5.7+20100313-2 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-3 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-8 libstdc++6-4.4-dev_4.4.4-8 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_160-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-15 libuuid1_2.17.2-3.1 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-20 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-2 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 procps_1:3.2.8-9 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2.1 tzdata_2010k-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100713-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.8 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.10 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.2.2 bsdutils_1:2.17.2-6 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.37 debconf-i18n_1.5.37 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2010.08.28 debianutils_3.4.2 diffutils_1:3.0-1 dpkg_1.15.8.8 dpkg-dev_1.15.8.8 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-6 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-3 libdpkg-perl_1.15.8.8 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.12-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-6 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-6 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2010o-1 util-linux_2.17.2-6 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -213,12 +222,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -233,60 +242,61 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
- dpkg-source --before-build bwa-0.5.8c
+dpkg-buildpackage: source version 0.5.9-1
+ dpkg-source --before-build bwa-0.5.9
dpkg-buildpackage: host architecture s390
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-s390-OQZpl7/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD is.c -o is.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD main.c -o main.o
+gcc -g -O2 -g -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-s390-AOoRjJ/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -299,7 +309,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -315,6 +325,7 @@ dh_installlogcheck -pbwa
dh_installchangelogs -pbwa ./ChangeLog
dh_installudev -pbwa
dh_lintian -pbwa
+dh_bugfiles -pbwa
dh_install -pbwa
dh_link -pbwa
dh_installmime -pbwa
@@ -329,63 +340,60 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bwa_0.5.8c-1_s390.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bwa_0.5.9-1_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 bwa-0.5.8c
+ dpkg-source --after-build bwa-0.5.9
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1241
+Build finished at 20110208-2035
-bwa_0.5.8c-1_s390.changes:
+bwa_0.5.9-1_s390.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: s390
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- 1d69601bc830b2b6985c49b7ddf1fce535d34e50 134418 bwa_0.5.8c-1_s390.deb
+ c03fba6d8c793d60d9f4e0eceb2a01d0f0e80761 140496 bwa_0.5.9-1_s390.deb
Checksums-Sha256:
- 47189341a017de9bdef58878a646f8d4481bf8e1b05252d0b3054cc59aef8a05 134418 bwa_0.5.8c-1_s390.deb
+ b27632cfa4225def55144e0794e00d6fb629ccb6a64270d1a5880ec75d0c2b67 140496 bwa_0.5.9-1_s390.deb
Files:
- 4f903c065146a9be454226ef1609ca29 134418 science optional bwa_0.5.8c-1_s390.deb
+ 96353fc0d7cbc1973f6adbc429d6c999 140496 science optional bwa_0.5.9-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_s390.deb
-─────────────────────
+bwa_0.5.9-1_s390.deb
+────────────────────
new debian package, version 2.0.
- size 134418 bytes: control archive= 942 bytes.
- 774 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 140496 bytes: control archive= 974 bytes.
+ 773 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 312
+ Installed-Size: 324
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -399,24 +407,25 @@ bwa_0.5.8c-1_s390.deb
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 2010-10-27 12:41 ./
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/bin/
--rwxr-xr-x root/root 196600 2010-10-27 12:41 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:41 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./usr/bin/
+-rwxr-xr-x root/root 206392 2011-02-08 20:35 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 20:35 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 20:35 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -425,9 +434,9 @@ drwxr-xr-x root/root 0 2010-10-27 12:41 ./usr/share/doc/bwa/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390-sbuild-97f0cde4-7fba-4981-b6d9-f8e39bfd0fde/build/buildd-bwa_0.5.8c-1-s390-OQZpl7
+Purging /var/lib/schroot/mount/sid-s390-sbuild-7b7874c9-18b1-486f-8396-68c0f241110c/build/buildd-bwa_0.5.9-1-s390-AOoRjJ
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1241
-Build needed 00:01:07, 2580k disc space
+Finished at 20110208-2035
+Build needed 00:01:07, 2620k disc space
diff --git a/sparc.log b/sparc.log
index 4b6f0ed..07fb4ef 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,4 +1,4 @@
-From buildd at lebrun.debian.org Wed Oct 27 12:40:47 2010
+From buildd at lebrun.debian.org Tue Feb 08 13:59:52 2011
Return-path: <buildd at lebrun.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,
@@ -6,56 +6,56 @@ 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 4.69) (envelope-from <buildd at lebrun.debian.org>)
- id 1PB5J8-0004vI-Ic
- for logs at buildd.debian.org; Wed, 27 Oct 2010 12:40:47 +0000
+ id 1Pmo6i-0002z6-6s
+ for logs at buildd.debian.org; Tue, 08 Feb 2011 13:59:52 +0000
Received: from lebrun.debian.org ([193.198.184.10])
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 merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at lebrun.debian.org>)
- id 1PB5J7-00074e-8S; Wed, 27 Oct 2010 12:40:45 +0000
+ id 1Pmo6g-000216-Ug; Tue, 08 Feb 2011 13:59:51 +0000
Received: from buildd by lebrun.debian.org with local (Exim 4.69)
(envelope-from <buildd at lebrun.debian.org>)
- id 1PB5J7-0008AD-Jv; Wed, 27 Oct 2010 12:40:45 +0000
+ id 1Pmo6f-0008S2-Kn; Tue, 08 Feb 2011 13:59:49 +0000
From: buildd on lebrun <buildd at lebrun.debian.org>
To: logs at buildd.debian.org,kibi at debian-ports.org
-Subject: Log for successful build of bwa_0.5.8c-1 on sparc (dist=unstable)
+Subject: Log for successful build of bwa_0.5.9-1 on sparc (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PB5J7-0008AD-Jv at lebrun.debian.org>
-Date: Wed, 27 Oct 2010 12:40:45 +0000
+Message-Id: <E1Pmo6f-0008S2-Kn at lebrun.debian.org>
+Date: Tue, 08 Feb 2011 13:59:49 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.8c-1 (sparc) 27 Oct 2010 12:38 ║
+║ bwa 0.5.9-1 (sparc) 08 Feb 2011 13:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.8c-1
+Version: 0.5.9-1
Architecture: sparc
-Chroot Build Dir: /var/lib/schroot/mount/sid-sparc-sbuild-4c51688f-7cd9-47eb-8f27-49a131d26722/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50
-Start Time: 20101027-1238
+Chroot Build Dir: /var/lib/schroot/mount/sid-sparc-sbuild-a20e677c-6f45-4c18-a629-3b02c202a5c8/build/buildd-bwa_0.5.9-1-sparc-nsEeFI
+Start Time: 20110208-1356
Get:1 http://debian.carnet.hr unstable Release.gpg [835B]
Get:2 http://incoming.debian.org unstable Release.gpg [835B]
Get:3 http://incoming.debian.org Release.gpg [835B]
Get:4 http://incoming.debian.org unstable Release [104kB]
Get:5 http://debian.carnet.hr unstable Release [104kB]
-Get:6 http://debian.carnet.hr unstable/main Packages [6699kB]
+Get:6 http://debian.carnet.hr unstable/main Packages [6837kB]
Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Packages [6699kB]
-Get:9 http://debian.carnet.hr unstable/contrib Packages [51.2kB]
-Get:10 http://debian.carnet.hr unstable/main Sources [4008kB]
-Get:11 http://debian.carnet.hr unstable/contrib Sources [38.7kB]
-Get:12 http://debian.carnet.hr unstable/non-free Sources [80.3kB]
-Get:13 http://incoming.debian.org unstable/contrib Packages [51.2kB]
-Get:14 http://incoming.debian.org unstable/main Sources [4008kB]
-Get:15 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:16 http://incoming.debian.org unstable/non-free Sources [80.3kB]
-Get:17 http://incoming.debian.org Packages [85.4kB]
-Get:18 http://incoming.debian.org Sources [23.4kB]
-Fetched 22.1MB in 23s (943kB/s)
+Get:8 http://incoming.debian.org unstable/main Packages [6837kB]
+Get:9 http://debian.carnet.hr unstable/contrib Packages [50.5kB]
+Get:10 http://debian.carnet.hr unstable/main Sources [4119kB]
+Get:11 http://debian.carnet.hr unstable/contrib Sources [38.6kB]
+Get:12 http://debian.carnet.hr unstable/non-free Sources [83.8kB]
+Get:13 http://incoming.debian.org unstable/contrib Packages [50.5kB]
+Get:14 http://incoming.debian.org unstable/main Sources [4119kB]
+Get:15 http://incoming.debian.org unstable/contrib Sources [38.6kB]
+Get:16 http://incoming.debian.org unstable/non-free Sources [83.8kB]
+Get:17 http://incoming.debian.org Packages [743kB]
+Get:18 http://incoming.debian.org Sources [49.9kB]
+Fetched 23.3MB in 25s (920kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,18 +74,18 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-Need to get 120kB of source archives.
-Get:1 http://incoming.debian.org bwa 0.5.8c-1 (dsc) [1905B]
-Get:2 http://incoming.debian.org bwa 0.5.8c-1 (tar) [114kB]
-Get:3 http://incoming.debian.org bwa 0.5.8c-1 (diff) [4005B]
-Fetched 120kB in 0s (138kB/s)
+Need to get 119kB of source archives.
+Get:1 http://incoming.debian.org bwa 0.5.9-1 (dsc) [1894B]
+Get:2 http://incoming.debian.org bwa 0.5.9-1 (tar) [114kB]
+Get:3 http://incoming.debian.org bwa 0.5.9-1 (diff) [3651B]
+Fetched 119kB in 0s (138kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -94,7 +94,7 @@ Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Checking for already installed source dependencies...
cdbs: missing
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.0
zlib1g-dev: missing
Checking for source dependency conflicts...
Installing positive dependencies: cdbs debhelper zlib1g-dev
@@ -103,8 +103,8 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
- po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff less www-browser libmail-box-perl
@@ -113,38 +113,41 @@ Recommended packages:
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0
- libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 71 not upgraded.
-Need to get 9997kB of archives.
-After this operation, 28.7MB of additional disk space will be used.
-Get:1 http://debian.carnet.hr unstable/main bsdmainutils 8.0.13 [203kB]
-Get:2 http://debian.carnet.hr unstable/main groff-base 1.20.1-10 [1146kB]
-Get:3 http://debian.carnet.hr unstable/main man-db 2.5.7-6 [1283kB]
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 19 newly installed, 0 to remove and 77 not upgraded.
+Need to get 9922kB of archives.
+After this operation, 28.6MB of additional disk space will be used.
+Get:1 http://debian.carnet.hr unstable/main bsdmainutils 8.2.2 [205kB]
+Get:2 http://incoming.debian.org groff-base 1.21-4 [1155kB]
+Get:3 http://debian.carnet.hr unstable/main libpipeline1 1.1.0-1 [35.0kB]
Get:4 http://debian.carnet.hr unstable/main libmagic1 5.04-5 [239kB]
Get:5 http://debian.carnet.hr unstable/main file 5.04-5 [49.5kB]
Get:6 http://debian.carnet.hr unstable/main gettext-base 0.18.1.1-3 [140kB]
-Get:7 http://debian.carnet.hr unstable/main libpcre3 8.02-1.1 [237kB]
-Get:8 http://debian.carnet.hr unstable/main libxml2 2.7.7.dfsg-4 [840kB]
-Get:9 http://debian.carnet.hr unstable/main html2text 1.3.2a-15 [100kB]
-Get:10 http://debian.carnet.hr unstable/main libglib2.0-0 2.24.2-1 [1074kB]
-Get:11 http://debian.carnet.hr unstable/main libcroco3 0.6.2-1 [119kB]
-Get:12 http://debian.carnet.hr unstable/main libunistring0 0.9.3-3 [424kB]
-Get:13 http://debian.carnet.hr unstable/main gettext 0.18.1.1-3 [2006kB]
-Get:14 http://debian.carnet.hr unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
-Get:15 http://debian.carnet.hr unstable/main po-debconf 1.0.16 [224kB]
-Get:16 http://debian.carnet.hr unstable/main debhelper 8.0.0 [454kB]
-Get:17 http://debian.carnet.hr unstable/main cdbs 0.4.89 [1240kB]
-Get:18 http://debian.carnet.hr unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [189kB]
+Get:7 http://debian.carnet.hr unstable/main libpcre3 8.12-1 [265kB]
+Get:8 http://incoming.debian.org man-db 2.5.9-4 [1007kB]
+Get:9 http://incoming.debian.org cdbs 0.4.92 [1268kB]
+Get:10 http://debian.carnet.hr unstable/main libxml2 2.7.8.dfsg-2 [840kB]
+Get:11 http://debian.carnet.hr unstable/main html2text 1.3.2a-15 [100kB]
+Get:12 http://debian.carnet.hr unstable/main libglib2.0-0 2.24.2-1 [1074kB]
+Get:13 http://debian.carnet.hr unstable/main libcroco3 0.6.2-1 [119kB]
+Get:14 http://debian.carnet.hr unstable/main libunistring0 0.9.3-3 [424kB]
+Get:15 http://debian.carnet.hr unstable/main gettext 0.18.1.1-3 [2006kB]
+Get:16 http://debian.carnet.hr unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
+Get:17 http://debian.carnet.hr unstable/main po-debconf 1.0.16+nmu1 [223kB]
+Get:18 http://debian.carnet.hr unstable/main debhelper 8.1.0 [552kB]
+Get:19 http://debian.carnet.hr unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [189kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9997kB in 7s (1418kB/s)
+Fetched 9922kB in 6s (1570kB/s)
Selecting previously deselected package bsdmainutils.
(Reading database ... 10174 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_sparc.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_sparc.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_sparc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_sparc.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_sparc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_sparc.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_sparc.deb) ...
Selecting previously deselected package file.
@@ -152,9 +155,9 @@ Unpacking file (from .../archives/file_5.04-5_sparc.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_sparc.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-1_sparc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_sparc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_sparc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -168,39 +171,40 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_sparc.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libpcre3 (8.12-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
-Setting up cdbs (0.4.89) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.0) ...
+Setting up cdbs (0.4.92) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-bpo.5-sparc64-smp sparc (sparc64)
Toolchain package versions: libc6-dev_2.11.2-2 dpkg-dev_1.15.7.2 linux-libc-dev_2.6.32-17 gcc-4.4_4.4.4-6 g++-4.4_4.4.4-6 binutils_2.20.1-12 libstdc++6-4.4-dev_4.4.4-6 libstdc++6_4.4.4-6
-Package versions: apt_0.7.25.3 base-files_5.8 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-12 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-4 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-6 dash_0.5.5.1-7 debconf_1.5.33 debconf-i18n_1.5.33 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.3 diffutils_1:3.0-1 dpkg_1.15.7.2 dpkg-dev_1.15.7.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-6 gcc_4:4.4.4-2 gcc-4.4_4.4.4-6 gcc-4.4-base_4.4.4-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-4 libc-bin_2.11.2-2 libc-dev-bin_2.11.2-2 libc6_2.11.2-2 libc6-dev_2.11.2-2 libc6-dev-sparc64_2.11.2-2 libc6-sparc64_2.11.2-2 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.26-3 libdpkg-perl_1.15.7.2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100527-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libncurses5_5.7+20100313-2 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-3 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.94-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-6 libstdc++6-4.4-dev_4.4.4-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-15 libuuid1_2.17.2-3.1 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-17 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-2 netbase_4.42 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-13 perl-base_5.10.1-13 perl-modules_5.10.1-13 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2 tzdata_2010j-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100527-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.7.25.3 base-files_5.8 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-12 bsdmainutils_8.2.2 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-4 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-6 dash_0.5.5.1-7 debconf_1.5.33 debconf-i18n_1.5.33 debfoster_2.7-1.1 debhelper_8.1.0 debian-archive-keyring_2009.01.31 debianutils_3.3 diffutils_1:3.0-1 dpkg_1.15.7.2 dpkg-dev_1.15.7.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-6 gcc_4:4.4.4-2 gcc-4.4_4.4.4-6 gcc-4.4-base_4.4.4-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-4 libc-bin_2.11.2-2 libc-dev-bin_2.11.2-2 libc6_2.11.2-2 libc6-dev_2.11.2-2 libc6-dev-sparc64_2.11.2-2 libc6-sparc64_2.11.2-2 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.26-3 libdpkg-perl_1.15.7.2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100527-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libncurses5_5.7+20100313-2 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-3 libpcre3_8.12-1 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.94-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-6 libstdc++6-4.4-dev_4.4.4-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-15 libuuid1_2.17.2-3.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-17 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-2 netbase_4.42 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-13 perl-base_5.10.1-13 perl-modules_5.10.1-13 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2 tzdata_2010j-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100527-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -212,12 +216,12 @@ 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 Wed Oct 27 12:20:51 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Feb 8 07:20:43 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.8c-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.8c
-dpkg-source: info: unpacking bwa_0.5.8c.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.8c-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.5.9-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.5.9
+dpkg-source: info: unpacking bwa_0.5.9.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.5.9-1.debian.tar.gz
Check disc space
────────────────
@@ -232,59 +236,60 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.8c-1
+dpkg-buildpackage: source version 0.5.9-1
dpkg-buildpackage: host architecture sparc
/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 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c/bwt_gen'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9/bwt_gen'
rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9/bwt_gen'
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9'
dh_clean
debian/rules build
test -x debian/rules
mkdir -p "."
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c'
-make[2]: Entering directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9'
+make[2]: Entering directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c/bwt_gen'
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -O2 -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50/bwa-0.5.8c'
+make[2]: Leaving directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9/bwt_gen'
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD is.c -o is.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
+gcc -c -g -O2 -g -O2 -DHAVE_PTHREAD main.c -o main.o
+gcc -g -O2 -g -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.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 main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
+make[1]: Leaving directory `/build/buildd-bwa_0.5.9-1-sparc-nsEeFI/bwa-0.5.9'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
/usr/bin/fakeroot debian/rules binary-arch
@@ -297,7 +302,7 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bwa.substvars
dh_installdirs -pbwa
-dh_installdocs -pbwa ./NEWS
+dh_installdocs -pbwa ./README ./NEWS
dh_installexamples -pbwa
dh_installman -pbwa
dh_installinfo -pbwa
@@ -313,6 +318,7 @@ dh_installlogcheck -pbwa
dh_installchangelogs -pbwa ./ChangeLog
dh_installudev -pbwa
dh_lintian -pbwa
+dh_bugfiles -pbwa
dh_install -pbwa
dh_link -pbwa
dh_installmime -pbwa
@@ -327,62 +333,59 @@ dh_gencontrol -pbwa
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -pbwa
dh_builddeb -pbwa
-dpkg-deb: building package `bwa' in `../bwa_0.5.8c-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bwa_0.5.8c-1_sparc.changes
+dpkg-deb: building package `bwa' in `../bwa_0.5.9-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bwa_0.5.9-1_sparc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101027-1240
+Build finished at 20110208-1359
-bwa_0.5.8c-1_sparc.changes:
+bwa_0.5.9-1_sparc.changes:
Format: 1.8
-Date: Wed, 27 Oct 2010 21:14:34 +0900
+Date: Tue, 08 Feb 2011 16:11:12 +0900
Source: bwa
Binary: bwa
Architecture: sparc
-Version: 0.5.8c-1
-Distribution: unstable
+Version: 0.5.9-1
+Distribution: sid
Urgency: low
Maintainer: sparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
-Closes: 601568
Changes:
- bwa (0.5.8c-1) unstable; urgency=low
+ bwa (0.5.9-1) unstable; urgency=low
.
- * Bug fix release, reverting the scoring system back to the one used in
- 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
- happen in principle. Such wrong cigars also incur errors in indel calling
- when samtools is in use (Closes: #601568).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * debian/copyright updated and reformatted.
+ * New usptream release
+ - Upstream moved to GitHub (debian/upstream-metadata.yaml).
+ - Checked copyright; one file was removed (debian/copyright).
+ * Migrated the Debian source package to Git (debian/control).
+ * Use Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
- a01b006d9252bc4f432cbd7b67cdabd289d2d25d 136048 bwa_0.5.8c-1_sparc.deb
+ c558fd30d6d49f216a0f70b59ab5baf98a1a5601 141936 bwa_0.5.9-1_sparc.deb
Checksums-Sha256:
- 1fd9baf3113a2b391b512892692a91a4942cacee9f4511efb30b72af685000a6 136048 bwa_0.5.8c-1_sparc.deb
+ b691b32ea45a1fed0d01c6ef6ecf3d622010b580326074bc53b8f4b5ca17bf10 141936 bwa_0.5.9-1_sparc.deb
Files:
- 4b4c11943be00e731d13f3379e1a80ab 136048 science optional bwa_0.5.8c-1_sparc.deb
+ 2b0e94456d4236ab33abde683ba0f6ff 141936 science optional bwa_0.5.9-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.8c-1_sparc.deb
-──────────────────────
+bwa_0.5.9-1_sparc.deb
+─────────────────────
new debian package, version 2.0.
- size 136048 bytes: control archive= 942 bytes.
- 775 bytes, 17 lines control
- 556 bytes, 9 lines md5sums
+ size 141936 bytes: control archive= 972 bytes.
+ 774 bytes, 17 lines control
+ 615 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.8c-1
+ Version: 0.5.9-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 308
+ Installed-Size: 316
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -396,24 +399,25 @@ bwa_0.5.8c-1_sparc.deb
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 2010-10-27 12:40 ./
-drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/
-drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/bin/
--rwxr-xr-x root/root 190520 2010-10-27 12:40 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/share/
-drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5294 2010-10-17 03:41 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 4336 2010-10-27 11:49 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/ChangeLog.gz
--rw-r--r-- root/root 17277 2010-10-17 03:41 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 759 2010-10-27 12:14 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/share/man/man1/
--rw-r--r-- root/root 7145 2010-10-27 12:40 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2010-10-17 03:41 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2010-10-17 03:41 ./usr/share/bwa/qualfa2fq.pl
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./usr/
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./usr/bin/
+-rwxr-xr-x root/root 198784 2011-02-08 13:59 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 5857 2011-01-25 00:00 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 2676 2011-02-08 07:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/ChangeLog.gz
+-rw-r--r-- root/root 17912 2011-01-25 00:00 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 634 2011-01-25 00:00 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 881 2011-02-08 07:11 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./usr/share/man/man1/
+-rw-r--r-- root/root 7554 2011-02-08 13:59 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-02-08 13:59 ./usr/share/bwa/
+-rwxr-xr-x root/root 3176 2011-01-25 00:00 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 616 2011-01-25 00:00 ./usr/share/bwa/qualfa2fq.pl
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -422,9 +426,9 @@ drwxr-xr-x root/root 0 2010-10-27 12:40 ./usr/share/bwa/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-4c51688f-7cd9-47eb-8f27-49a131d26722/build/buildd-bwa_0.5.8c-1-sparc-Hw8J50
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-a20e677c-6f45-4c18-a629-3b02c202a5c8/build/buildd-bwa_0.5.9-1-sparc-nsEeFI
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101027-1240
-Build needed 00:02:38, 2444k disc space
+Finished at 20110208-1359
+Build needed 00:02:46, 2480k disc space
--
Burrows-Wheeler Aligner
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