[med-svn] [SCM] bwa branch, experimental-meta, updated. 553e45f3a9078b5faf0a8146aaae0da02dce046a
Charles Plessy
plessy at debian.org
Tue Nov 22 05:25:34 UTC 2011
The following commit has been merged in the experimental-meta branch:
commit 553e45f3a9078b5faf0a8146aaae0da02dce046a
Author: Charles Plessy <plessy at debian.org>
Date: Tue Nov 22 14:23:31 2011 +0900
Uploaded bwa_0.6.0-2_amd64.changes to experimental.
diff --git a/amd64.log b/amd64.log
index 0537a68..66ec23a 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,18 +1,18 @@
sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on anx191
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.6.0-1 (amd64) 14 Nov 2011 19:29 ║
+║ bwa 0.6.0-2 (amd64) 22 Nov 2011 11:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.6.0-1
-Source Version: 0.6.0-1
+Version: 0.6.0-2
+Source Version: 0.6.0-2
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/bwa-DsC1CL/bwa-0.6.0' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/bwa-DsC1CL' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-a638d509-5b19-4d6e-bf69-2ce494596aed' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/bwa-l2eBQa/bwa-0.6.0' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bwa-l2eBQa' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-d82180c0-d625-4bf2-9f6c-9ed4fceb1a7d' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -35,14 +35,14 @@ Reading state information...
Local sources
─────────────
-bwa_0.6.0-1.dsc exists in .; copying to chroot
+bwa_0.6.0-2.dsc exists in .; copying to chroot
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-uq8zfI/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-5wL1sG/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -58,7 +58,7 @@ sbuild-build-depends-core-dummy is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-bwa-dummy' in `/«BUILDDIR»/resolver-co7OV6/apt_archive/sbuild-build-depends-bwa-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-bwa-dummy' in `/«BUILDDIR»/resolver-kG7mZ2/apt_archive/sbuild-build-depends-bwa-dummy.deb'.
OK
Reading package lists...
@@ -72,8 +72,8 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
debhelper file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf zlib1g-dev
+ libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0
+ libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
dh-make gettext-doc groff less www-browser libmail-box-perl
Recommended packages:
@@ -81,19 +81,21 @@ Recommended packages:
libmail-sendmail-perl
The following NEW packages will be installed:
debhelper file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf sbuild-build-depends-bwa-dummy zlib1g-dev
+ libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0
+ libxml2 man-db po-debconf sbuild-build-depends-bwa-dummy zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/9162 kB of archives.
-After this operation, 25.4 MB of additional disk space will be used.
+0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/9380 kB of archives.
+After this operation, 25.7 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 10824 files and directories currently installed.)
+(Reading database ... 10825 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ...
Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_amd64.deb) ...
Selecting previously unselected package libcroco3.
@@ -119,14 +121,15 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously unselected package sbuild-build-depends-bwa-dummy.
Unpacking sbuild-build-depends-bwa-dummy (from .../sbuild-build-depends-bwa-dummy.deb) ...
Setting up libpipeline1 (1.2.0-5) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
@@ -141,7 +144,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
+Setting up debhelper (8.9.11) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ...
@@ -150,8 +153,8 @@ Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 2.6.39-bpo.2-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-6
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 libgpm2_1.20.4-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-6 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu1 readline-common_6.2-7 sbuild-build-depends-bwa-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.1.1-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-11-20-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 libgpm2_1.20.4-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-11-20-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-5 perl-base_5.14.2-5 perl-modules_5.14.2-5 po-debconf_1.0.16+nmu1 readline-common_6.2-7 sbuild-build-depends-bwa-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -161,10 +164,9 @@ Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (bwa_0.6.0-1.dsc)
+dpkg-source: warning: extracting unsigned source package (bwa_0.6.0-2.dsc)
dpkg-source: info: extracting bwa in bwa-0.6.0
-dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
+dpkg-source: info: unpacking bwa_0.6.0-2.tar.gz
Check disc space
────────────────
@@ -181,7 +183,7 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-a638d509-5b19-4d6e-bf69-2ce494596aed
+SCHROOT_SESSION_ID=sid-amd64-sbuild-d82180c0-d625-4bf2-9f6c-9ed4fceb1a7d
SCHROOT_UID=31051
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -193,7 +195,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.6.0-1
+dpkg-buildpackage: source version 0.6.0-2
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture amd64
@@ -206,22 +208,21 @@ rm -f gmon.out *.o a.out bwa *~ *.a
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_clean
dpkg-source -b bwa-0.6.0
-dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: building bwa using existing ./bwa_0.6.0.orig.tar.bz2
-dpkg-source: info: building bwa in bwa_0.6.0-1.debian.tar.gz
-dpkg-source: info: building bwa in bwa_0.6.0-1.dsc
+dpkg-source: info: using source format `3.0 (native)'
+dpkg-source: info: building bwa in bwa_0.6.0-2.tar.gz
+dpkg-source: info: building bwa in bwa_0.6.0-2.dsc
debian/rules build
dh build
dh_testdir
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory `/«PKGBUILDDIR»'
-dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro" DFLAGS="-DHAVE_PTHREAD"
make[2]: Entering directory `/«PKGBUILDDIR»'
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
QSufSort.c: In function 'QSufSortSuffixSort':
QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
@@ -230,9 +231,9 @@ bwt_gen.c: In function 'BWTIncConstructFromPacked':
bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
bwtio.c: In function 'bwt_restore_bwt':
bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
@@ -243,33 +244,33 @@ bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute
bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
bntseq.c: In function 'bns_restore_core':
bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
bwtmisc.c: In function 'bwa_pac2cspac_core':
bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwtmisc.c: In function 'bwt_pac2bwt':
bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwtmisc.c: In function 'bwa_seq_len':
bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD stdaln.c -o stdaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD stdaln.c -o stdaln.o
stdaln.c: In function 'aln_local_core':
stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
stdaln.c: In function 'aln_extend_core':
stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwase.c -o bwase.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwase.c -o bwase.o
bwase.c: In function 'bwa_aln2seq_core':
bwase.c:74:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
bwase.c: In function 'bwa_print_sam1':
@@ -281,7 +282,7 @@ bwase.c:624:9: warning: ignoring return value of 'fread', declared with attribut
bwase.c: In function 'bwa_refine_gapped':
bwase.c:310:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwase.c:316:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwape.c -o bwape.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwape.c -o bwape.o
bwape.c: In function 'bwa_sai2sam_pe_core':
bwape.c:683:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwape.c:686:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
@@ -291,22 +292,22 @@ bwape.c:527:8: warning: ignoring return value of 'fread', declared with attribut
bwape.c: In function 'bwa_cal_pac_pos_pe':
bwape.c:312:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bwape.c:316:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD kstring.c -o kstring.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
bwtsw2_aux.c: In function 'gen_cigar':
bwtsw2_aux.c:186:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
bwtsw2_aux.c: In function 'bsw2_aln':
bwtsw2_aux.c:734:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD fastmap.c -o fastmap.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o
-gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD main.c -o main.o
-gcc -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o fastmap.o bwtsw2_pair.o main.o -o bwa -lm -lz -lpthread
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bamlite.c -o bamlite.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD fastmap.c -o fastmap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD main.c -o main.o
+gcc -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o fastmap.o bwtsw2_pair.o main.o -o bwa -lm -lz -lpthread
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test
@@ -357,13 +358,13 @@ dh binary
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums
dh_builddeb
-dpkg-deb: building package `bwa' in `../bwa_0.6.0-1_amd64.deb'.
- dpkg-genchanges >../bwa_0.6.0-1_amd64.changes
+dpkg-deb: building package `bwa' in `../bwa_0.6.0-2_amd64.deb'.
+ dpkg-genchanges >../bwa_0.6.0-2_amd64.changes
dpkg-genchanges: including full source code in upload
dpkg-source --after-build bwa-0.6.0
-dpkg-buildpackage: full upload (original source is included)
+dpkg-buildpackage: full upload; Debian-native package (full source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-1929
+Build finished at 20111122-1139
Finished
────────
@@ -375,57 +376,57 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.6.0-1_amd64.changes:
+bwa_0.6.0-2_amd64.changes:
──────────────────────────
Format: 1.8
-Date: Mon, 14 Nov 2011 19:28:44 +0900
+Date: Tue, 22 Nov 2011 11:32:11 +0900
Source: bwa
Binary: bwa
Architecture: source amd64
-Version: 0.6.0-1
+Version: 0.6.0-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
+Closes: 648803
Changes:
- bwa (0.6.0-1) experimental; urgency=low
+ bwa (0.6.0-2) experimental; urgency=low
.
- [9ce640c] New upstream release (not to use in a production pipeline).
- [e641dd6] Corrected the name of the file downloaded by uscan.
- [4ada685] Pass Dpkg build flags to the compiler through Debhelper 9. Thanks, Niels Thykier!
+ [9410de3] Disable SSE2 everywhere except on amd64 (Closes: #648803).
+ [fb4c559] Reimplementation of Standard SW for when SSE2 is unavailable.
+ cherry picked from upstream commit 182cb2e.
+ This commit modifies upstream sources.
+ [9c93ccd] Use native format to bypass mandatory patch system.
Checksums-Sha1:
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- bed98c8e29dbad66633d6cab78544dd887525fc1 129917 bwa_0.6.0.orig.tar.bz2
- 53581a760b4ada06a5b9d2ad99e5266f189e6673 4313 bwa_0.6.0-1.debian.tar.gz
- 8a4560b51febf50ba12cdaa195c05dbf292bc7a2 151896 bwa_0.6.0-1_amd64.deb
+ faa001f0b81f62a1a74062336db232e2bf0d8cc4 795 bwa_0.6.0-2.dsc
+ 6c49a7a61d424bde502a03fb38858e8eebd588f1 169209 bwa_0.6.0-2.tar.gz
+ 09224646b17bf5092150a41330b110201de9c346 152102 bwa_0.6.0-2_amd64.deb
Checksums-Sha256:
- f1fe44aea44fffe2f394c897fb78005bfa80753901849a6806c9037b7e20e43e 1041 bwa_0.6.0-1.dsc
- e30b063b2ebfe7cfd2c431f37a6c35700b953c13d9c7088b89edcb4d56e62c7b 129917 bwa_0.6.0.orig.tar.bz2
- 009c44be30a73c9df9045850357087bf512109b8f660be2224d48ebf4b7e6bf6 4313 bwa_0.6.0-1.debian.tar.gz
- d1dafd8a5d59a6f9fc685d9875ec35db9048466aa1eeace6d8eb7dd1b5d3416c 151896 bwa_0.6.0-1_amd64.deb
+ 1b3f463655cc1e3ab3bcc02c91e6143f7ebb70c4d73eb500d086268cc3cb6a43 795 bwa_0.6.0-2.dsc
+ 8d917434fd8ccfff3685f9aab1214c512985f55d1ee8b8c7933fa358b184f5b5 169209 bwa_0.6.0-2.tar.gz
+ 7984ef9c940d40b76781e487e45439a4de29823a588faa07de63aaf33f71dbf1 152102 bwa_0.6.0-2_amd64.deb
Files:
- 031e9a879cbc27359fe0027705443d96 1041 science optional bwa_0.6.0-1.dsc
- 89dc57e3791044e661742cad988eb203 129917 science optional bwa_0.6.0.orig.tar.bz2
- 9b285d6b6415c7f7ebb806389243c809 4313 science optional bwa_0.6.0-1.debian.tar.gz
- 53fe875efc2288841ba96fa51ef2efc8 151896 science optional bwa_0.6.0-1_amd64.deb
+ c7fe8760f6941189a548c11a3bb26b75 795 science optional bwa_0.6.0-2.dsc
+ 7d8655d45605071b3cf22c402208fbf9 169209 science optional bwa_0.6.0-2.tar.gz
+ b39ec9278cf86460cdb78f7745ac7d12 152102 science optional bwa_0.6.0-2_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.6.0-1_amd64.deb
+bwa_0.6.0-2_amd64.deb
─────────────────────
new debian package, version 2.0.
- size 151896 bytes: control archive= 991 bytes.
+ size 152102 bytes: control archive= 990 bytes.
774 bytes, 17 lines control
610 bytes, 10 lines md5sums
Package: bwa
- Version: 0.6.0-1
+ Version: 0.6.0-2
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 296
@@ -442,25 +443,25 @@ bwa_0.6.0-1_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 2011-11-14 19:29 ./
-drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/bin/
--rwxr-xr-x root/root 219752 2011-11-14 19:29 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/share/man/man1/
--rw-r--r-- root/root 7745 2011-11-14 19:29 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/share/bwa/
--rwxr-xr-x root/root 616 2011-11-13 10:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2011-11-13 10:07 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 730 2011-11-13 10:07 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17912 2011-11-13 10:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 6680 2011-11-13 10:07 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 2785 2011-11-14 19:27 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 634 2011-11-13 10:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 1299 2011-11-14 19:28 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./usr/
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./usr/bin/
+-rwxr-xr-x root/root 219752 2011-11-22 11:39 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./usr/share/man/man1/
+-rw-r--r-- root/root 7745 2011-11-22 11:39 ./usr/share/man/man1/bwa.1.gz
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./usr/share/bwa/
+-rwxr-xr-x root/root 616 2011-11-22 10:55 ./usr/share/bwa/qualfa2fq.pl
+-rwxr-xr-x root/root 3176 2011-11-22 10:55 ./usr/share/bwa/solid2fastq.pl
+-rwxr-xr-x root/root 730 2011-11-22 10:55 ./usr/share/bwa/xa2multi.pl
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-22 11:39 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 17912 2011-11-22 10:55 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 6680 2011-11-22 10:55 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 2785 2011-11-22 10:55 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 634 2011-11-22 10:55 ./usr/share/doc/bwa/README
+-rw-r--r-- root/root 1471 2011-11-22 11:32 ./usr/share/doc/bwa/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -471,10 +472,11 @@ drwxr-xr-x root/root 0 2011-11-14 19:29 ./usr/share/doc/bwa/
lintian
───────
+W: bwa source: native-package-with-dash-version
W: bwa source: package-needs-versioned-debhelper-build-depends 9
P: bwa source: unversioned-copyright-format-uri http://dep.debian.net/deps/dep5/
+W: bwa source: debian-watch-file-in-native-package
W: bwa source: debian-watch-file-should-use-sf-redirector line 4
-W: bwa: debian-changelog-line-too-long line 3
W: bwa: manpage-has-errors-from-man usr/share/man/man1/bwa.1.gz around line 328: table wider than line width
I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:7
I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:49
@@ -504,12 +506,12 @@ Building dependency tree...
Reading state information...
The following packages will be REMOVED:
debhelper* file* gettext* gettext-base* groff-base* html2text*
- intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpcre3* libpipeline1*
- libunistring0* libxml2* man-db* po-debconf* sbuild-build-depends-bwa-dummy*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 18 to remove and 0 not upgraded.
-After this operation, 25.4 MB disk space will be freed.
-(Reading database ... 12058 files and directories currently installed.)
+ intltool-debian* libcroco3* libffi5* libglib2.0-0* libmagic1* libpcre3*
+ libpipeline1* libunistring0* libxml2* man-db* po-debconf*
+ sbuild-build-depends-bwa-dummy* zlib1g-dev*
+0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded.
+After this operation, 25.7 MB disk space will be freed.
+(Reading database ... 12065 files and directories currently installed.)
Removing sbuild-build-depends-bwa-dummy ...
Removing debhelper ...
Removing file ...
@@ -527,6 +529,8 @@ Removing libcroco3 ...
Purging configuration files for libcroco3 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
+Removing libffi5 ...
+Purging configuration files for libffi5 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
Removing libpcre3 ...
@@ -544,18 +548,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 3520
-Build-Time: 10
+Build-Space: 3552
+Build-Time: 11
Distribution: unstable
-Install-Time: 23
-Job: bwa_0.6.0-1.dsc
+Install-Time: 32
+Job: bwa_0.6.0-2.dsc
Lintian: pass
Package: bwa
-Package-Time: 37
-Source-Version: 0.6.0-1
-Space: 3520
+Package-Time: 48
+Source-Version: 0.6.0-2
+Space: 3552
Status: successful
-Version: 0.6.0-1
+Version: 0.6.0-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-1929
-Build needed 00:00:37, 3520k disc space
+Finished at 20111122-1139
+Build needed 00:00:48, 3552k disc space
diff --git a/changes b/changes
index 40409eb..41938e5 100644
--- a/changes
+++ b/changes
@@ -2,53 +2,53 @@
Hash: SHA256
Format: 1.8
-Date: Mon, 14 Nov 2011 19:28:44 +0900
+Date: Tue, 22 Nov 2011 11:32:11 +0900
Source: bwa
Binary: bwa
Architecture: source amd64
-Version: 0.6.0-1
-Distribution: unstable
+Version: 0.6.0-2
+Distribution: experimental
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
+Closes: 648803
Changes:
- bwa (0.6.0-1) experimental; urgency=low
+ bwa (0.6.0-2) experimental; urgency=low
.
- [9ce640c] New upstream release (not to use in a production pipeline).
- [e641dd6] Corrected the name of the file downloaded by uscan.
- [4ada685] Pass Dpkg build flags to the compiler through Debhelper 9. Thanks, Niels Thykier!
+ [9410de3] Disable SSE2 everywhere except on amd64 (Closes: #648803).
+ [fb4c559] Reimplementation of Standard SW for when SSE2 is unavailable.
+ cherry picked from upstream commit 182cb2e.
+ This commit modifies upstream sources.
+ [9c93ccd] Use native format to bypass mandatory patch system.
Checksums-Sha1:
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+ 5f192c1147232c0b8fa581fa398167b518ac7e33adffc9245112f2291d9573fd 1681 bwa_0.6.0-2.dsc
+ 8d917434fd8ccfff3685f9aab1214c512985f55d1ee8b8c7933fa358b184f5b5 169209 bwa_0.6.0-2.tar.gz
+ 7984ef9c940d40b76781e487e45439a4de29823a588faa07de63aaf33f71dbf1 152102 bwa_0.6.0-2_amd64.deb
Files:
- 9a336e657c14e6edf2fe418e8c6120cd 1927 science optional bwa_0.6.0-1.dsc
- 89dc57e3791044e661742cad988eb203 129917 science optional bwa_0.6.0.orig.tar.bz2
- 9b285d6b6415c7f7ebb806389243c809 4313 science optional bwa_0.6.0-1.debian.tar.gz
- 53fe875efc2288841ba96fa51ef2efc8 151896 science optional bwa_0.6.0-1_amd64.deb
+ 91ef0cb0d0d4ebeb33f28ae784c4e672 1681 science optional bwa_0.6.0-2.dsc
+ 7d8655d45605071b3cf22c402208fbf9 169209 science optional bwa_0.6.0-2.tar.gz
+ b39ec9278cf86460cdb78f7745ac7d12 152102 science optional bwa_0.6.0-2_amd64.deb
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diff --git a/dsc b/dsc
index fcfccd0..773a6be 100644
--- a/dsc
+++ b/dsc
@@ -1,11 +1,11 @@
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
-Format: 3.0 (quilt)
+Format: 3.0 (native)
Source: bwa
Binary: bwa
Architecture: any
-Version: 0.6.0-1
+Version: 0.6.0-2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>, Andreas Tille <tille at debian.org>
Dm-Upload-Allowed: yes
@@ -17,29 +17,26 @@ Build-Depends: debhelper (>= 8.9.4~), zlib1g-dev
Package-List:
bwa deb science optional
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--
Burrows-Wheeler Aligner
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