[med-svn] [htslib] 01/01: htslib (1.0-1) experimental; urgency=low
Charles Plessy
plessy at moszumanska.debian.org
Mon Aug 18 12:05:30 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch debian/build/experimental/amd64
in repository htslib.
commit a5db8c7e091c36878fdb41f1968b864629761d6f
Author: Charles Plessy <plessy at debian.org>
Date: Mon Aug 18 20:55:53 2014 +0900
htslib (1.0-1) experimental; urgency=low
cc559b8 Merged with upstream's master branch.
74b9d7b Build on the master branch.
04815a7 New major version (libhts0 -> libhts1).
98c18ca Updated symbols file.
22fef0c Install pkgconfig file.
420896b Override PACKAGE_VERSION to avoid tags with a slash in the name.
79b5d4e Use the Debian package version as PACKAGE_VERSION.
72b5c4a Finally use the 3.0 (quilt) format in single-debian-patch mode.
d870946 Adjusted substitution variables following dpkg's warnings.
9469458 Removed debug command accidentally introduced.
8c7f7d4 Replace the old tabix package from the tabix source package.
-- Charles Plessy <plessy at debian.org> Sun, 17 Aug 2014 20:12:28 +0900
---
log | 1731 +++++++++++++++++++++++++++++++++----------------------------------
1 file changed, 845 insertions(+), 886 deletions(-)
diff --git a/log b/log
index 1adc856..690ef30 100644
--- a/log
+++ b/log
@@ -1,20 +1,20 @@
-sbuild (Debian sbuild) 0.64.0 (17 May 2013) on aqwa.igloo
+sbuild (Debian sbuild) 0.64.1 (13 Oct 2013) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ htslib 0.2.0~rc3-1 (amd64) 16 nov. 2013 15:36 ║
+║ htslib 1.0-1 (amd64) 18 août 2014 20:48 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: htslib
-Version: 0.2.0~rc3-1
-Source Version: 0.2.0~rc3-1
+Version: 1.0-1
+Source Version: 1.0-1
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/htslib-LDWG20/htslib-0.2.0~rc3' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/htslib-LDWG20' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-3623818a-285b-44c6-8b58-d098bced0492' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/htslib-9Ji_et/htslib-1.0' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/htslib-9Ji_et' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-db4e5189-cb5f-4991-b8ba-7f91a666e68f' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -28,7 +28,35 @@ Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+The following packages will be upgraded:
+ binutils cpp debfoster g++ gcc libgmp10
+6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Need to get 253 kB/3608 kB of archives.
+After this operation, 9216 B of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main libgmp10 amd64 2:6.0.0+dfsg-6 [253 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 253 kB in 0s (586 kB/s)
+(Reading database ... 11135 files and directories currently installed.)
+Preparing to unpack .../libgmp10_2%3a6.0.0+dfsg-6_amd64.deb ...
+Unpacking libgmp10:amd64 (2:6.0.0+dfsg-6) over (2:6.0.0+dfsg-4) ...
+Preparing to unpack .../binutils_2.24.51.20140814-2_amd64.deb ...
+Unpacking binutils (2.24.51.20140814-2) over (2.24.51.20140814-1) ...
+Preparing to unpack .../cpp_4%3a4.9.1-2_amd64.deb ...
+Unpacking cpp (4:4.9.1-2) over (4:4.9.1-1) ...
+Preparing to unpack .../debfoster_2.7-2_amd64.deb ...
+Unpacking debfoster (2.7-2) over (2.7-1.2) ...
+Preparing to unpack .../gcc_4%3a4.9.1-2_amd64.deb ...
+Removing old gcc doc directory.
+Unpacking gcc (4:4.9.1-2) over (4:4.9.1-1) ...
+Preparing to unpack .../g++_4%3a4.9.1-2_amd64.deb ...
+Unpacking g++ (4:4.9.1-2) over (4:4.9.1-1) ...
+Setting up libgmp10:amd64 (2:6.0.0+dfsg-6) ...
+Setting up binutils (2.24.51.20140814-2) ...
+Setting up cpp (4:4.9.1-2) ...
+Setting up debfoster (2.7-2) ...
+Setting up gcc (4:4.9.1-2) ...
+Setting up g++ (4:4.9.1-2) ...
+Processing triggers for libc-bin (2.19-9) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -38,14 +66,14 @@ Reading state information...
Local sources
─────────────
-htslib_0.2.0~rc3-1.dsc exists in .; copying to chroot
+htslib_1.0-1.dsc exists in .; copying to chroot
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-d1H_ig/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-mnuFN7/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -61,15 +89,16 @@ The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/768 B of archives.
+Need to get 0 B/822 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 11123 files and directories currently installed.)
-Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
+(Reading database ... 11135 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), dh-exec, zlib1g-dev
-Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), dh-exec, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-htslib-dummy' in `/«BUILDDIR»/resolver-vtjHRp/apt_archive/sbuild-build-depends-htslib-dummy.deb'.
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-exec, zlib1g-dev
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-exec, zlib1g-dev
+dpkg-deb: building package `sbuild-build-depends-htslib-dummy' in `/«BUILDDIR»/resolver-lvcEPq/apt_archive/sbuild-build-depends-htslib-dummy.deb'.
OK
Reading package lists...
@@ -96,84 +125,107 @@ The following NEW packages will be installed:
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
sbuild-build-depends-htslib-dummy zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/8210 kB of archives.
-After this operation, 25.5 MB of additional disk space will be used.
+Need to get 948 kB/8948 kB of archives.
+After this operation, 27.1 MB of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main libcroco3 amd64 0.6.8-3 [135 kB]
+Get:2 http://ftp.jp.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 948 kB in 1s (486 kB/s)
Selecting previously unselected package libpipeline1:amd64.
-(Reading database ... 11123 files and directories currently installed.)
-Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.4-1_amd64.deb) ...
+(Reading database ... 11135 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.3.0-1_amd64.deb ...
+Unpacking libpipeline1:amd64 (1.3.0-1) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-3_amd64.deb) ...
+Preparing to unpack .../groff-base_1.22.2-6_amd64.deb ...
+Unpacking groff-base (1.22.2-6) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_amd64.deb) ...
+Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ...
+Unpacking bsdmainutils (9.0.5) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.5-2_amd64.deb) ...
+Preparing to unpack .../man-db_2.6.7.1-1_amd64.deb ...
+Unpacking man-db (2.6.7.1-1) ...
Selecting previously unselected package libasprintf0c2:amd64.
-Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.3.1-1_amd64.deb) ...
+Preparing to unpack .../libasprintf0c2_0.19.2-1_amd64.deb ...
+Unpacking libasprintf0c2:amd64 (0.19.2-1) ...
Selecting previously unselected package libmagic1:amd64.
-Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.14-2_amd64.deb) ...
+Preparing to unpack .../libmagic1_1%3a5.19-1_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.19-1) ...
Selecting previously unselected package libxml2:amd64.
-Unpacking libxml2:amd64 (from .../libxml2_2.9.1+dfsg1-3_amd64.deb) ...
+Preparing to unpack .../libxml2_2.9.1+dfsg1-4_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.1+dfsg1-4) ...
Selecting previously unselected package libffi6:amd64.
-Unpacking libffi6:amd64 (from .../libffi6_3.0.13-4_amd64.deb) ...
+Preparing to unpack .../libffi6_3.1-2_amd64.deb ...
+Unpacking libffi6:amd64 (3.1-2) ...
Selecting previously unselected package libglib2.0-0:amd64.
-Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.36.4-1_amd64.deb) ...
+Preparing to unpack .../libglib2.0-0_2.40.0-4_amd64.deb ...
+Unpacking libglib2.0-0:amd64 (2.40.0-4) ...
Selecting previously unselected package libcroco3:amd64.
-Unpacking libcroco3:amd64 (from .../libcroco3_0.6.8-2_amd64.deb) ...
+Preparing to unpack .../libcroco3_0.6.8-3_amd64.deb ...
+Unpacking libcroco3:amd64 (0.6.8-3) ...
Selecting previously unselected package libunistring0:amd64.
-Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ...
+Preparing to unpack .../libunistring0_0.9.3-5.2_amd64.deb ...
+Unpacking libunistring0:amd64 (0.9.3-5.2) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.14-2_amd64.deb) ...
+Preparing to unpack .../file_1%3a5.19-1_amd64.deb ...
+Unpacking file (1:5.19-1) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.3.1-1_amd64.deb) ...
+Preparing to unpack .../gettext-base_0.19.2-1_amd64.deb ...
+Unpacking gettext-base (0.19.2-1) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.3.1-1_amd64.deb) ...
+Preparing to unpack .../gettext_0.19.2-1_amd64.deb ...
+Unpacking gettext (0.19.2-1) ...
Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.1) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
+Unpacking po-debconf (1.0.16+nmu3) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20131110_all.deb) ...
+Preparing to unpack .../debhelper_9.20140817_all.deb ...
+Unpacking debhelper (9.20140817) ...
Selecting previously unselected package zlib1g-dev:amd64.
-Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.8.dfsg-1_amd64.deb) ...
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2) ...
Selecting previously unselected package dh-exec.
-Unpacking dh-exec (from .../dh-exec_0.12_amd64.deb) ...
+Preparing to unpack .../dh-exec_0.13_amd64.deb ...
+Unpacking dh-exec (0.13) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
-Unpacking sbuild-build-depends-htslib-dummy (from .../sbuild-build-depends-htslib-dummy.deb) ...
-Setting up libpipeline1:amd64 (1.2.4-1) ...
-Setting up groff-base (1.22.2-3) ...
+Preparing to unpack .../sbuild-build-depends-htslib-dummy.deb ...
+Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
+Setting up libpipeline1:amd64 (1.3.0-1) ...
+Setting up groff-base (1.22.2-6) ...
Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.5-2) ...
+Setting up man-db (2.6.7.1-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libasprintf0c2:amd64 (0.18.3.1-1) ...
-Setting up libmagic1:amd64 (1:5.14-2) ...
-Setting up libxml2:amd64 (2.9.1+dfsg1-3) ...
-Setting up libffi6:amd64 (3.0.13-4) ...
-Setting up libglib2.0-0:amd64 (2.36.4-1) ...
+Setting up libasprintf0c2:amd64 (0.19.2-1) ...
+Setting up libmagic1:amd64 (1:5.19-1) ...
+Setting up libxml2:amd64 (2.9.1+dfsg1-4) ...
+Setting up libffi6:amd64 (3.1-2) ...
+Setting up libglib2.0-0:amd64 (2.40.0-4) ...
No schema files found: doing nothing.
-Setting up libcroco3:amd64 (0.6.8-2) ...
-Setting up libunistring0:amd64 (0.9.3-5) ...
-Setting up file (1:5.14-2) ...
-Setting up gettext-base (0.18.3.1-1) ...
-Setting up gettext (0.18.3.1-1) ...
+Setting up libcroco3:amd64 (0.6.8-3) ...
+Setting up libunistring0:amd64 (0.9.3-5.2) ...
+Setting up file (1:5.19-1) ...
+Setting up gettext-base (0.19.2-1) ...
+Setting up gettext (0.19.2-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20131110) ...
-Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ...
-Setting up dh-exec (0.12) ...
+Setting up po-debconf (1.0.16+nmu3) ...
+Setting up debhelper (9.20140817) ...
+Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2) ...
+Setting up dh-exec (0.13) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
-Processing triggers for libc-bin ...
+Processing triggers for libc-bin (2.19-9) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.10-1-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.23.90.20131017-1 dpkg-dev_1.17.1 g++-4.8_4.8.2-4 gcc-4.8_4.8.2-4 libc6-dev_2.17-96 libstdc++-4.8-dev_4.8.2-4 libstdc++6_4.8.2-4 linux-libc-dev_3.11.8-1
-Package versions: apt_0.9.12.1 base-files_7.2 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.23.90.20131017-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpp_4:4.8.1-3 cpp-4.8_4.8.2-4 dash_0.5.7-3 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20131110 debian-archive-keyring_2012.4 debianutils_4.4 dh-exec_0.12 diffutils_1:3.3-1 dpkg_1.17.1 dpkg-dev_1.17.1 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 eatmydata_26-2 fakeroot_1.20-1 [...]
+Kernel: Linux 3.14-1-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.24.51.20140814-2 dpkg-dev_1.17.12 g++-4.9_4.9.1-7 gcc-4.9_4.9.1-7 libc6-dev_2.19-9 libstdc++-4.9-dev_4.9.1-7 libstdc++6_4.9.1-7 linux-libc-dev_3.14.15-2
+Package versions: apt_1.0.6 base-files_7.5 base-passwd_3.5.33 bash_4.3-8 binutils_2.24.51.20140814-2 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.21-1.2 cpp_4:4.9.1-2 cpp-4.9_4.9.1-7 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2012.4 debianutils_4.4 dh-exec_0.13 diffutils_1:3.3-1 dpkg_1.17.12 dpkg-dev_1.17.12 e2fslibs_1.42.11-2 e2fsprogs_1.42.11-2 eatmydata_26-2 fakeroot_1.20.1-1 fi [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -183,21 +235,11 @@ Package versions: apt_0.9.12.1 base-files_7.2 base-passwd_3.5.28 bash_4.2+dfsg-1
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (htslib_0.2.0~rc3-1.dsc)
-dpkg-source: info: extracting htslib in htslib-0.2.0~rc3
-dpkg-source: info: unpacking htslib_0.2.0~rc3.orig.tar.gz
-dpkg-source: info: applying htslib_0.2.0~rc3-1.diff.gz
-dpkg-source: info: upstream files that have been modified:
- htslib-0.2.0~rc3/bgzf.c
- htslib-0.2.0~rc3/cram/cram_io.c
- htslib-0.2.0~rc3/hfile.c
- htslib-0.2.0~rc3/hfile.h
- htslib-0.2.0~rc3/hts.c
- htslib-0.2.0~rc3/htslib/bgzf.h
- htslib-0.2.0~rc3/htslib/hts.h
- htslib-0.2.0~rc3/htslib/vcfutils.h
- htslib-0.2.0~rc3/sam.c
- htslib-0.2.0~rc3/vcfutils.c
+dpkg-source: warning: extracting unsigned source package (htslib_1.0-1.dsc)
+dpkg-source: info: extracting htslib in htslib-1.0
+dpkg-source: info: unpacking htslib_1.0.orig.tar.gz
+dpkg-source: info: unpacking htslib_1.0-1.debian.tar.xz
+dpkg-source: info: applying debian-changes
Check disc space
────────────────
@@ -215,7 +257,7 @@ SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=unstable-amd64-sbuild-3623818a-285b-44c6-8b58-d098bced0492
+SCHROOT_SESSION_ID=unstable-amd64-sbuild-db4e5189-cb5f-4991-b8ba-7f91a666e68f
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -231,36 +273,37 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package htslib
-dpkg-buildpackage: source version 0.2.0~rc3-1
-dpkg-buildpackage: source distribution unstable
+dpkg-buildpackage: source version 1.0-1
+dpkg-buildpackage: source distribution experimental
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build htslib-0.2.0~rc3
+ dpkg-source --before-build htslib-1.0
dpkg-buildpackage: host architecture amd64
+dpkg-source: info: using options from htslib-1.0/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 distclean
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f test/*.tmp test/*.tmp.*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.so libhts.so.*
-rm -f libhts.a test/fieldarith test/hfile test/test_view test/test-vcf-api test/test-vcf-sweep
-rm -f TAGS
-make[1]: Leaving directory `/«PKGBUILDDIR»'
- debian/rules override_dh_clean
-make[1]: Entering directory `/«PKGBUILDDIR»'
-chmod ugo+x debian/libhts0.install debian/libhts-dev.install
-dh_clean
- rm -f debian/libhts0.substvars
- rm -f debian/libhts0.*.debhelper
- rm -rf debian/libhts0/
+rm -f libhts.a bgzip tabix test/fieldarith test/hfile test/sam test/test_view test/test-vcf-api test/test-vcf-sweep
+rm -f TAGS *-uninstalled.pc
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean
+ rm -f debian/libhts1.substvars
+ rm -f debian/libhts1.*.debhelper
+ rm -rf debian/libhts1/
rm -f debian/libhts-dev.substvars
rm -f debian/libhts-dev.*.debhelper
rm -rf debian/libhts-dev/
rm -f debian/htslib-test.substvars
rm -f debian/htslib-test.*.debhelper
rm -rf debian/htslib-test/
+ rm -f debian/tabix.substvars
+ rm -f debian/tabix.*.debhelper
+ rm -rf debian/tabix/
rm -f debian/*.debhelper.log
rm -f debian/files
find . \( \( -type f -a \
@@ -271,341 +314,120 @@ dh_clean
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
rm -f *-stamp
-make[1]: Leaving directory `/«PKGBUILDDIR»'
- dpkg-source -b htslib-0.2.0~rc3
-dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1)
-dpkg-source: info: using source format `1.0'
-dpkg-source: info: building htslib using existing htslib_0.2.0~rc3.orig.tar.gz
-dpkg-source: info: building htslib in htslib_0.2.0~rc3-1.diff.gz
-dpkg-source: warning: executable mode 0755 of 'debian/libhts-dev.install' will not be represented in diff
-dpkg-source: warning: executable mode 0755 of 'debian/libhts0.install' will not be represented in diff
-dpkg-source: warning: the diff modifies the following upstream files:
- bgzf.c
- cram/cram_io.c
- hfile.c
- hfile.h
- hts.c
- htslib/bgzf.h
- htslib/hts.h
- htslib/vcfutils.h
- sam.c
- vcfutils.c
-dpkg-source: info: use the '3.0 (quilt)' format to have separate and documented changes to upstream files, see dpkg-source(1)
-dpkg-source: info: building htslib in htslib_0.2.0~rc3-1.dsc
+ dpkg-source -b htslib-1.0
+dpkg-source: info: using options from htslib-1.0/debian/source/options: --single-debian-patch
+dpkg-source: info: using source format `3.0 (quilt)'
+dpkg-source: info: building htslib using existing ./htslib_1.0.orig.tar.gz
+dpkg-source: info: building htslib in htslib_1.0-1.debian.tar.xz
+dpkg-source: info: building htslib in htslib_1.0-1.dsc
debian/rules build
dh build
dh_testdir
dh_auto_configure
debian/rules override_dh_auto_build
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
- CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
- make -j1 "CFLAGS=-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
-make[2]: Entering directory `/«PKGBUILDDIR»'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
-In file included from knetfile.c:46:0:
-knetfile.c: In function 'kftp_send_cmd':
-htslib/knetfile.h:9:37: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- #define netwrite(fd, ptr, len) write(fd, ptr, len)
- ^
-knetfile.c:236:2: note: in expansion of macro 'netwrite'
- netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
- ^
-knetfile.c: In function 'khttp_connect_file':
-htslib/knetfile.h:9:37: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- #define netwrite(fd, ptr, len) write(fd, ptr, len)
- ^
-knetfile.c:415:2: note: in expansion of macro 'netwrite'
- netwrite(fp->fd, buf, l);
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
-bgzf.c: In function 'bgzf_index_load':
-bgzf.c:888:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx);
- ^
-bgzf.c:899:18: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].caddr = ed_swap_8(x);
- ^
-bgzf.c:900:18: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].uaddr = ed_swap_8(x);
- ^
-bgzf.c:907:18: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].caddr = x;
- ^
-bgzf.c:908:18: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].uaddr = x;
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
-echo '#define HTS_VERSION "0.0.1"' > version.h
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
-hts.c: In function 'hts_idx_load_local':
-hts.c:823:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(magic, 1, 4, fp);
- ^
-hts.c:824:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&n, 4, 1, fp);
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o razf.o razf.c
-razf.c: In function 'razf_flush':
-razf.c:223:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
- ^
-razf.c:236:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
- ^
-razf.c: In function '_razf_write':
-razf.c:203:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
- ^
-razf.c: In function 'razf_open_r':
-razf.c:423:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, &end, sizeof(int64_t));
- ^
-razf.c:431:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, &end, sizeof(int64_t));
- ^
-razf.c: In function 'load_zindex':
-razf.c:124:6: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, &rz->index->size, sizeof(int));
- ^
-razf.c:133:6: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
- ^
-razf.c:139:6: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
- ^
-razf.c: In function 'razf_close':
-razf.c:818:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, &rz->in, sizeof(int64_t));
- ^
-razf.c:819:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, &rz->out, sizeof(int64_t));
- ^
-razf.c:822:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, &v64, sizeof(int64_t));
- ^
-razf.c:824:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, &v64, sizeof(int64_t));
- ^
-razf.c: In function 'razf_end_flush':
-razf.c:260:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
- ^
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- if(is_be) write(fd, &rz->index->size, sizeof(int));
- ^
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(fd, &v32, sizeof(uint32_t));
- ^
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
- ^
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
-sam.c: In function 'sam_hdr_write':
-sam.c:461:11: warning: ignoring return value of 'hwrite', declared with attribute warn_unused_result [-Wunused-result]
- hwrite(fp->fp.hfile, fp->line.s, fp->line.l);
- ^
-sam.c:464:9: warning: ignoring return value of 'hflush', declared with attribute warn_unused_result [-Wunused-result]
- hflush(fp->fp.hfile);
- ^
-sam.c: In function 'sam_write1':
-sam.c:758:9: warning: ignoring return value of 'hwrite', declared with attribute warn_unused_result [-Wunused-result]
- hwrite(fp->fp.hfile, fp->line.s, fp->line.l);
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/md5.o cram/md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/thread_pool.o cram/thread_pool.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/vlen.o cram/vlen.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/zfio.o cram/zfio.c
-ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o razf.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+# re-try later LDLIBS=-lhts \
+ PACKAGE_VERSION="1.0-1" \
+ libdir=/usr/lib/x86_64-linux-gnu
+ make -j1 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
+echo '#define HTS_VERSION "1.0"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/md5.o cram/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/thread_pool.o cram/thread_pool.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/vlen.o cram/vlen.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/zfio.o cram/zfio.c
+ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o kfunc.pico kfunc.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o knetfile.pico knetfile.c
-In file included from knetfile.c:46:0:
-knetfile.c: In function 'kftp_send_cmd':
-htslib/knetfile.h:9:37: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- #define netwrite(fd, ptr, len) write(fd, ptr, len)
- ^
-knetfile.c:236:2: note: in expansion of macro 'netwrite'
- netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
- ^
-knetfile.c: In function 'khttp_connect_file':
-htslib/knetfile.h:9:37: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- #define netwrite(fd, ptr, len) write(fd, ptr, len)
- ^
-knetfile.c:415:2: note: in expansion of macro 'netwrite'
- netwrite(fp->fd, buf, l);
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o kstring.pico kstring.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o bgzf.pico bgzf.c
-bgzf.c: In function 'bgzf_index_load':
-bgzf.c:888:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx);
- ^
-bgzf.c:899:18: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].caddr = ed_swap_8(x);
- ^
-bgzf.c:900:18: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].uaddr = ed_swap_8(x);
- ^
-bgzf.c:907:18: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].caddr = x;
- ^
-bgzf.c:908:18: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].uaddr = x;
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o faidx.pico faidx.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile.pico hfile.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile_net.pico hfile_net.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hts.pico hts.c
-hts.c: In function 'hts_idx_load_local':
-hts.c:823:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(magic, 1, 4, fp);
- ^
-hts.c:824:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
- fread(&n, 4, 1, fp);
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o razf.pico razf.c
-razf.c: In function 'razf_flush':
-razf.c:223:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
- ^
-razf.c:236:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
- ^
-razf.c: In function '_razf_write':
-razf.c:203:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
- ^
-razf.c: In function 'razf_open_r':
-razf.c:423:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, &end, sizeof(int64_t));
- ^
-razf.c:431:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, &end, sizeof(int64_t));
- ^
-razf.c: In function 'load_zindex':
-razf.c:124:6: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, &rz->index->size, sizeof(int));
- ^
-razf.c:133:6: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
- ^
-razf.c:139:6: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
- read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
- ^
-razf.c: In function 'razf_close':
-razf.c:818:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, &rz->in, sizeof(int64_t));
- ^
-razf.c:819:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, &rz->out, sizeof(int64_t));
- ^
-razf.c:822:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, &v64, sizeof(int64_t));
- ^
-razf.c:824:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, &v64, sizeof(int64_t));
- ^
-razf.c: In function 'razf_end_flush':
-razf.c:260:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
- ^
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- if(is_be) write(fd, &rz->index->size, sizeof(int));
- ^
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(fd, &v32, sizeof(uint32_t));
- ^
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
- ^
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
- write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o sam.pico sam.c
-sam.c: In function 'sam_hdr_write':
-sam.c:461:11: warning: ignoring return value of 'hwrite', declared with attribute warn_unused_result [-Wunused-result]
- hwrite(fp->fp.hfile, fp->line.s, fp->line.l);
- ^
-sam.c:464:9: warning: ignoring return value of 'hflush', declared with attribute warn_unused_result [-Wunused-result]
- hflush(fp->fp.hfile);
- ^
-sam.c: In function 'sam_write1':
-sam.c:758:9: warning: ignoring return value of 'hwrite', declared with attribute warn_unused_result [-Wunused-result]
- hwrite(fp->fp.hfile, fp->line.s, fp->line.l);
- ^
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcf_sweep.pico vcf_sweep.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o tbx.pico tbx.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcf.pico vcf.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcfutils.pico vcfutils.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_index.pico cram/cram_index.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_io.pico cram/cram_io.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/files.pico cram/files.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/mFILE.pico cram/mFILE.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/md5.pico cram/md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/sam_header.pico cram/sam_header.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/thread_pool.pico cram/thread_pool.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/vlen.pico cram/vlen.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/zfio.pico cram/zfio.c
-gcc -shared -Wl,-soname,libhts.so.0 -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico razf.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/md5.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/sam_header [...]
-ln -sf libhts.so libhts.so.0
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o kfunc.pico kfunc.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o knetfile.pico knetfile.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o kstring.pico kstring.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o bgzf.pico bgzf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o faidx.pico faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile.pico hfile.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile_net.pico hfile_net.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hts.pico hts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o sam.pico sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcf_sweep.pico vcf_sweep.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o tbx.pico tbx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcf.pico vcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcfutils.pico vcfutils.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_index.pico cram/cram_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_io.pico cram/cram_io.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/files.pico cram/files.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/mFILE.pico cram/mFILE.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/md5.pico cram/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/sam_header.pico cram/sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/thread_pool.pico cram/thread_pool.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/vlen.pico cram/vlen.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/zfio.pico cram/zfio.c
+gcc -shared -Wl,-soname,libhts.so.1 -pthread -Wl,-z,relro -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/md5.pico cram/open_trace_file.pico cram/pooled_alloc.pico cra [...]
+ln -sf libhts.so libhts.so.1
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c
+gcc -pthread -Wl,-z,relro -o bgzip bgzip.o libhts.a -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
+gcc -pthread -Wl,-z,relro -o tabix tabix.o libhts.a -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -pthread -Wl,-z,relro -o test/fieldarith test/fieldarith.o libhts.a -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
gcc -Wl,-z,relro -o test/hfile test/hfile.o libhts.a -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c
+gcc -pthread -Wl,-z,relro -o test/sam test/sam.o libhts.a -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
gcc -pthread -Wl,-z,relro -o test/test_view test/test_view.o libhts.a -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -pthread -Wl,-z,relro -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -pthread -Wl,-z,relro -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test
make -j1 test
-make[2]: Entering directory `/«PKGBUILDDIR»'
+make[2]: Entering directory '/«PKGBUILDDIR»'
test/fieldarith test/fieldarith.sam
test/hfile
+test/sam
cd test && ./test_view.pl
=== Testing aux#aux.sam, ref aux.fa ===
@@ -614,11 +436,11 @@ cd test && ./test_view.pl
./compare_sam.pl aux#aux.sam aux#aux.tmp.bam.sam_
./test_view -t aux.fa -S -C aux#aux.sam > aux#aux.tmp.cram
./test_view -D aux#aux.tmp.cram > aux#aux.tmp.cram.sam_
- ./compare_sam.pl aux#aux.sam aux#aux.tmp.cram.sam_
+ ./compare_sam.pl -nomd aux#aux.sam aux#aux.tmp.cram.sam_
./test_view -t aux.fa -C aux#aux.tmp.bam > aux#aux.tmp.bam.cram
./test_view -b -D aux#aux.tmp.bam.cram > aux#aux.tmp.bam.cram.bam
./test_view aux#aux.tmp.bam.cram.bam > aux#aux.tmp.bam.cram.bam.sam_
- ./compare_sam.pl aux#aux.sam aux#aux.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd aux#aux.sam aux#aux.tmp.bam.cram.bam.sam_
=== Testing c1#bounds.sam, ref c1.fa ===
./test_view -S -b c1#bounds.sam > c1#bounds.tmp.bam
@@ -626,11 +448,11 @@ cd test && ./test_view.pl
./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#bounds.sam > c1#bounds.tmp.cram
./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
- ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.cram.sam_
+ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -t c1.fa -C c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
- ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
=== Testing c1#clip.sam, ref c1.fa ===
./test_view -S -b c1#clip.sam > c1#clip.tmp.bam
@@ -638,11 +460,11 @@ cd test && ./test_view.pl
./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#clip.sam > c1#clip.tmp.cram
./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
- ./compare_sam.pl c1#clip.sam c1#clip.tmp.cram.sam_
+ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -t c1.fa -C c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
- ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
=== Testing c1#pad1.sam, ref c1.fa ===
./test_view -S -b c1#pad1.sam > c1#pad1.tmp.bam
@@ -650,11 +472,11 @@ cd test && ./test_view.pl
./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#pad1.sam > c1#pad1.tmp.cram
./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
- ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.cram.sam_
+ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -t c1.fa -C c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
- ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
=== Testing c1#pad2.sam, ref c1.fa ===
./test_view -S -b c1#pad2.sam > c1#pad2.tmp.bam
@@ -662,11 +484,11 @@ cd test && ./test_view.pl
./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#pad2.sam > c1#pad2.tmp.cram
./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
- ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.cram.sam_
+ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -t c1.fa -C c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
- ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
=== Testing c1#pad3.sam, ref c1.fa ===
./test_view -S -b c1#pad3.sam > c1#pad3.tmp.bam
@@ -674,11 +496,11 @@ cd test && ./test_view.pl
./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#pad3.sam > c1#pad3.tmp.cram
./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
- ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.cram.sam_
+ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -t c1.fa -C c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
- ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
=== Testing ce#1.sam, ref ce.fa ===
./test_view -S -b ce#1.sam > ce#1.tmp.bam
@@ -686,11 +508,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#1.sam > ce#1.tmp.cram
./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
- ./compare_sam.pl ce#1.sam ce#1.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -t ce.fa -C ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#1.sam ce#1.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
=== Testing ce#2.sam, ref ce.fa ===
./test_view -S -b ce#2.sam > ce#2.tmp.bam
@@ -698,11 +520,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#2.sam > ce#2.tmp.cram
./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
- ./compare_sam.pl ce#2.sam ce#2.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -t ce.fa -C ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#2.sam ce#2.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
=== Testing ce#5.sam, ref ce.fa ===
./test_view -S -b ce#5.sam > ce#5.tmp.bam
@@ -710,11 +532,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#5.sam > ce#5.tmp.cram
./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
- ./compare_sam.pl ce#5.sam ce#5.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -t ce.fa -C ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#5.sam ce#5.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
=== Testing ce#5b.sam, ref ce.fa ===
./test_view -S -b ce#5b.sam > ce#5b.tmp.bam
@@ -722,11 +544,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#5b.sam > ce#5b.tmp.cram
./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
- ./compare_sam.pl ce#5b.sam ce#5b.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -t ce.fa -C ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
=== Testing ce#large_seq.sam, ref ce.fa ===
./test_view -S -b ce#large_seq.sam > ce#large_seq.tmp.bam
@@ -734,11 +556,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
- ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -t ce.fa -C ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
=== Testing ce#tag_depadded.sam, ref ce.fa ===
./test_view -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
@@ -746,11 +568,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
- ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -t ce.fa -C ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
=== Testing ce#tag_padded.sam, ref ce.fa ===
./test_view -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
@@ -758,11 +580,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
- ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -t ce.fa -C ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
=== Testing ce#unmap.sam, ref ce.fa ===
./test_view -S -b ce#unmap.sam > ce#unmap.tmp.bam
@@ -770,11 +592,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#unmap.sam > ce#unmap.tmp.cram
./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
- ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -t ce.fa -C ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
=== Testing ce#unmap1.sam, ref ce.fa ===
./test_view -S -b ce#unmap1.sam > ce#unmap1.tmp.bam
@@ -782,11 +604,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
- ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -t ce.fa -C ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
=== Testing ce#unmap2.sam, ref ce.fa ===
./test_view -S -b ce#unmap2.sam > ce#unmap2.tmp.bam
@@ -794,11 +616,11 @@ cd test && ./test_view.pl
./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
- ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.cram.sam_
+ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -t ce.fa -C ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
- ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
=== Testing xx#blank.sam, ref xx.fa ===
./test_view -S -b xx#blank.sam > xx#blank.tmp.bam
@@ -806,11 +628,11 @@ cd test && ./test_view.pl
./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#blank.sam > xx#blank.tmp.cram
./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
- ./compare_sam.pl xx#blank.sam xx#blank.tmp.cram.sam_
+ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -t xx.fa -C xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
- ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
=== Testing xx#large_aux.sam, ref xx.fa ===
./test_view -S -b xx#large_aux.sam > xx#large_aux.tmp.bam
@@ -818,11 +640,11 @@ cd test && ./test_view.pl
./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
- ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.cram.sam_
+ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -t xx.fa -C xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
- ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
=== Testing xx#large_aux2.sam, ref xx.fa ===
./test_view -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
@@ -830,11 +652,11 @@ cd test && ./test_view.pl
./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
- ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
+ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -t xx.fa -C xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
- ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
=== Testing xx#minimal.sam, ref xx.fa ===
./test_view -S -b xx#minimal.sam > xx#minimal.tmp.bam
@@ -842,11 +664,11 @@ cd test && ./test_view.pl
./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#minimal.sam > xx#minimal.tmp.cram
./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
- ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.cram.sam_
+ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -t xx.fa -C xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
- ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
=== Testing xx#pair.sam, ref xx.fa ===
./test_view -S -b xx#pair.sam > xx#pair.tmp.bam
@@ -854,11 +676,11 @@ cd test && ./test_view.pl
./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#pair.sam > xx#pair.tmp.cram
./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
- ./compare_sam.pl xx#pair.sam xx#pair.tmp.cram.sam_
+ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -t xx.fa -C xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
- ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
=== Testing xx#rg.sam, ref xx.fa ===
./test_view -S -b xx#rg.sam > xx#rg.tmp.bam
@@ -866,11 +688,11 @@ cd test && ./test_view.pl
./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#rg.sam > xx#rg.tmp.cram
./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
- ./compare_sam.pl xx#rg.sam xx#rg.tmp.cram.sam_
+ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -t xx.fa -C xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
- ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
=== Testing xx#triplet.sam, ref xx.fa ===
./test_view -S -b xx#triplet.sam > xx#triplet.tmp.bam
@@ -878,11 +700,11 @@ cd test && ./test_view.pl
./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#triplet.sam > xx#triplet.tmp.cram
./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
- ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.cram.sam_
+ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -t xx.fa -C xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
- ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
=== Testing xx#unsorted.sam, ref xx.fa ===
./test_view -S -b xx#unsorted.sam > xx#unsorted.tmp.bam
@@ -890,22 +712,22 @@ cd test && ./test_view.pl
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
- ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.cram.sam_
+ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -t xx.fa -C xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
- ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
+ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
Successes 240
Failures 0
cd test && ./test.pl
test_vcf_api:
- /«PKGBUILDDIR»/test/test-vcf-api /tmp/ZTPQ6jFdh9/test-vcf-api.bcf
+ /«PKGBUILDDIR»/test/test-vcf-api /tmp/NP8coRiKLj/test-vcf-api.bcf
.. ok
test_vcf_sweep:
- /«PKGBUILDDIR»/test/test-vcf-sweep /tmp/ZTPQ6jFdh9/test-vcf-api.bcf
+ /«PKGBUILDDIR»/test/test-vcf-sweep /tmp/NP8coRiKLj/test-vcf-api.bcf
.. ok
@@ -914,53 +736,67 @@ Number of tests:
passed .. 2
failed .. 0
-make[2]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Leaving directory '/«PKGBUILDDIR»'
rm -f test/*.tmp test/*.tmp.* test/*.o test/*.dSYM \
test/fieldarith test/hfile test/test_view test/test-vcf-api test/test-vcf-sweep
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
- rm -f debian/libhts0.substvars
- rm -f debian/libhts0.*.debhelper
- rm -rf debian/libhts0/
+ rm -f debian/libhts1.substvars
+ rm -f debian/libhts1.*.debhelper
+ rm -rf debian/libhts1/
rm -f debian/libhts-dev.substvars
rm -f debian/libhts-dev.*.debhelper
rm -rf debian/libhts-dev/
rm -f debian/htslib-test.substvars
rm -f debian/htslib-test.*.debhelper
rm -rf debian/htslib-test/
+ rm -f debian/tabix.substvars
+ rm -f debian/tabix.*.debhelper
+ rm -rf debian/tabix/
debian/rules override_dh_auto_install
-make[1]: Entering directory `/«PKGBUILDDIR»'
-dh_auto_install -- prefix=/usr
- install -d debian/libhts0
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm /«PKGBUILDDIR»/test/sam
+dh_auto_install -- \
+ prefix=/usr \
+ libdir=/usr/lib/x86_64-linux-gnu \
+ PACKAGE_VERSION="1.0-1"
+ install -d debian/libhts1
install -d debian/libhts-dev
install -d debian/htslib-test
- make -j1 install DESTDIR=/«BUILDDIR»/htslib-0.2.0\~rc3/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
-make[2]: Entering directory `/«PKGBUILDDIR»'
-mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/include/htslib /«PKGBUILDDIR»/debian/tmp/usr/lib /«PKGBUILDDIR»/debian/tmp/usr/share/man/man5
-install -p -m 644 libhts.so /«PKGBUILDDIR»/debian/tmp/usr/lib/libhts.so.0.0.1
-ln -sf libhts.so.0.0.1 /«PKGBUILDDIR»/debian/tmp/usr/lib/libhts.so
-ln -sf libhts.so.0.0.1 /«PKGBUILDDIR»/debian/tmp/usr/lib/libhts.so.0
+ install -d debian/tabix
+ make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr libdir=/usr/lib/x86_64-linux-gnu PACKAGE_VERSION=1.0-1
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/include /«PKGBUILDDIR»/debian/tmp/usr/include/htslib /«PKGBUILDDIR»/debian/tmp/usr/lib/x86_64-linux-gnu /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man5 /«PKGBUILDDIR»/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig
+install -p -m 644 libhts.so /«PKGBUILDDIR»/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.0-1
+ln -sf libhts.so.1.0-1 /«PKGBUILDDIR»/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so
+ln -sf libhts.so.1.0-1 /«PKGBUILDDIR»/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1
+sed -e 's#@includedir@#/usr/include#g;s#@libdir@#/usr/lib/x86_64-linux-gnu#g;s#@PACKAGE_VERSION@#1.0-1#g' htslib.pc.in > /«PKGBUILDDIR»/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc
+chmod 644 /«PKGBUILDDIR»/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc
+install -p bgzip tabix /«PKGBUILDDIR»/debian/tmp/usr/bin
install -p -m 644 htslib/*.h /«PKGBUILDDIR»/debian/tmp/usr/include/htslib
-install -p -m 644 libhts.a /«PKGBUILDDIR»/debian/tmp/usr/lib/libhts.a
+install -p -m 644 libhts.a /«PKGBUILDDIR»/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a
+install -p -m 644 *.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
install -p -m 644 *.5 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man5
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_install
- install -d debian/libhts0/usr/lib/x86_64-linux-gnu/
- cp -a debian/tmp/usr/lib/libhts.so.0 debian/libhts0/usr/lib/x86_64-linux-gnu//
- cp -a debian/tmp/usr/lib/libhts.so.0.0.1 debian/libhts0/usr/lib/x86_64-linux-gnu//
- install -d debian/libhts-dev/usr/include/
- cp -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include//
- install -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/
- cp -a debian/tmp/usr/lib/libhts.a debian/libhts-dev/usr/lib/x86_64-linux-gnu//
- cp -a debian/tmp/usr/lib/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu//
- install -d debian/libhts-dev/usr/share/man/man5/
- cp -a debian/tmp/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5//
- cp -a debian/tmp/usr/share/man/man5/sam.5 debian/libhts-dev/usr/share/man/man5//
- cp -a debian/tmp/usr/share/man/man5/vcf.5 debian/libhts-dev/usr/share/man/man5//
+ install -d debian/libhts1/usr/lib/x86_64-linux-gnu
+ cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1 debian/libhts1/usr/lib/x86_64-linux-gnu/
+ cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.0-1 debian/libhts1/usr/lib/x86_64-linux-gnu/
+ install -d debian/libhts-dev/usr/include
+ cp -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/
+ install -d debian/libhts-dev/usr/lib/x86_64-linux-gnu
+ cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a debian/libhts-dev/usr/lib/x86_64-linux-gnu/
+ cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu/
+ install -d debian/libhts-dev/usr/share/man/man5
+ cp -a debian/tmp/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5/
+ cp -a debian/tmp/usr/share/man/man5/sam.5 debian/libhts-dev/usr/share/man/man5/
+ cp -a debian/tmp/usr/share/man/man5/vcf.5 debian/libhts-dev/usr/share/man/man5/
+ install -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig
+ cp -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig/
install -d debian/htslib-test//usr/share/htslib-test
cp -a ./test/aux\#aux.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/aux.fa debian/htslib-test//usr/share/htslib-test/
@@ -988,6 +824,7 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
cp -a ./test/fieldarith.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/fieldarith.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/hfile.c debian/htslib-test//usr/share/htslib-test/
+ cp -a ./test/sam.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-api.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-api.out debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-sweep.c debian/htslib-test//usr/share/htslib-test/
@@ -1005,17 +842,23 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
cp -a ./test/xx\#unsorted.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx.fa debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx.fa.fai debian/htslib-test//usr/share/htslib-test/
+ install -d debian/tabix/usr/bin
+ cp -a ./tabix debian/tabix/usr/bin/
+ cp -a ./bgzip debian/tabix/usr/bin/
dh_installdocs
- install -g 0 -o 0 -d debian/libhts0/usr/share/doc/libhts0
- install -g 0 -o 0 -m 644 -p debian/copyright debian/libhts0/usr/share/doc/libhts0/copyright
+ install -g 0 -o 0 -d debian/libhts1/usr/share/doc/libhts1
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/libhts1/usr/share/doc/libhts1/copyright
install -g 0 -o 0 -d debian/libhts-dev/usr/share/doc/libhts-dev
install -g 0 -o 0 -m 644 -p debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright
install -g 0 -o 0 -d debian/htslib-test/usr/share/doc/htslib-test
install -g 0 -o 0 -m 644 -p debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright
+ install -g 0 -o 0 -d debian/tabix/usr/share/doc/tabix
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/tabix/usr/share/doc/tabix/copyright
dh_installchangelogs
- install -o 0 -g 0 -p -m644 debian/changelog debian/libhts0/usr/share/doc/libhts0/changelog.Debian
+ install -o 0 -g 0 -p -m644 debian/changelog debian/libhts1/usr/share/doc/libhts1/changelog.Debian
install -o 0 -g 0 -p -m644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian
install -o 0 -g 0 -p -m644 debian/changelog debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian
+ install -o 0 -g 0 -p -m644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian
dh_installman
man --recode UTF-8 ./vcf\.5 > vcf\.5\.new
chmod 644 vcf.5.new
@@ -1026,18 +869,25 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
man --recode UTF-8 ./sam\.5 > sam\.5\.new
chmod 644 sam.5.new
mv -f sam.5.new sam.5
+ install -d debian/tabix/usr/share/man/man1/
+ install -p -m644 tabix.1 debian/tabix/usr/share/man/man1/tabix.1
+ man --recode UTF-8 ./tabix\.1 > tabix\.1\.new
+ chmod 644 tabix.1.new
+ mv -f tabix.1.new tabix.1
dh_perl
(grep -s -v perl:Depends debian/htslib-test.substvars; echo perl:Depends=perl) > debian/htslib-test.substvars.new
mv debian/htslib-test.substvars.new debian/htslib-test.substvars
dh_link
- rm -f debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0
- ln -sf libhts.so.0.0.1 debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0
+ rm -f debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1
+ ln -sf libhts.so.1.0-1 debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1
rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so
- ln -sf libhts.so.0.0.1 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so
+ ln -sf libhts.so.1.0-1 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so
+ rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz
+ ln -sf tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz
dh_compress
- cd debian/libhts0
- chmod a-x usr/share/doc/libhts0/changelog.Debian
- gzip -9nf usr/share/doc/libhts0/changelog.Debian
+ cd debian/libhts1
+ chmod a-x usr/share/doc/libhts1/changelog.Debian
+ gzip -9nf usr/share/doc/libhts1/changelog.Debian
cd '/«PKGBUILDDIR»'
cd debian/libhts-dev
chmod a-x usr/share/man/man5/vcf.5 usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/doc/libhts-dev/changelog.Debian
@@ -1047,18 +897,22 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
chmod a-x usr/share/doc/htslib-test/changelog.Debian
gzip -9nf usr/share/doc/htslib-test/changelog.Debian
cd '/«PKGBUILDDIR»'
+ cd debian/tabix
+ chmod a-x usr/share/man/man1/tabix.1 usr/share/doc/tabix/changelog.Debian
+ gzip -9nf usr/share/man/man1/tabix.1 usr/share/doc/tabix/changelog.Debian
+ cd '/«PKGBUILDDIR»'
dh_fixperms
- find debian/libhts0 -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
- find debian/libhts0 ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
- find debian/libhts0/usr/share/doc -type f ! -regex 'debian/libhts0/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
- find debian/libhts0/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
- find debian/libhts0/usr/share/man debian/libhts0/usr/man/ debian/libhts0/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/libhts0 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/libhts0/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/libhts0/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/libhts0 -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/libhts0/usr/lib/perl5 debian/libhts0/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
- find debian/libhts0/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
+ find debian/libhts1 -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/libhts1 ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/libhts1/usr/share/doc -type f ! -regex 'debian/libhts1/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/libhts1/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/libhts1/usr/share/man debian/libhts1/usr/man/ debian/libhts1/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/libhts1 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/libhts1/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/libhts1/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/libhts1 -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/libhts1/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/libhts1/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/libhts1/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/libhts-dev -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/libhts-dev ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libhts-dev/usr/share/doc -type f ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
@@ -1068,7 +922,7 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
find debian/libhts-dev/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/libhts-dev/usr/lib/perl5 debian/libhts-dev/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/libhts-dev/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/libhts-dev/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/libhts-dev/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/htslib-test -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/htslib-test ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
@@ -1079,94 +933,113 @@ make[1]: Leaving directory `/«PKGBUILDDIR»'
find debian/htslib-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/htslib-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/htslib-test -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/htslib-test/usr/lib/perl5 debian/htslib-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/htslib-test/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/htslib-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/htslib-test/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
+ find debian/tabix -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/tabix ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/tabix/usr/share/doc -type f ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/tabix/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/tabix/usr/share/man debian/tabix/usr/man/ debian/tabix/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/tabix -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/tabix/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/tabix/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/tabix -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/tabix/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/tabix/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/tabix/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/tabix/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_strip
- strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1
+ strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.0-1
strip --strip-debug debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.a
+ strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix
+ strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip
dh_makeshlibs
- rm -f debian/libhts0/DEBIAN/shlibs
- install -d debian/libhts0/DEBIAN
- echo 'libhts 0 libhts0' >>debian/libhts0/DEBIAN/shlibs
- echo "# Automatically added by dh_makeshlibs">> debian/libhts0.postinst.debhelper
- sed "" /usr/share/debhelper/autoscripts/postinst-makeshlibs >> debian/libhts0.postinst.debhelper
- echo '# End automatically added section' >> debian/libhts0.postinst.debhelper
- echo "# Automatically added by dh_makeshlibs">> debian/libhts0.postrm.debhelper
- sed "" /usr/share/debhelper/autoscripts/postrm-makeshlibs >> debian/libhts0.postrm.debhelper
- echo '# End automatically added section' >> debian/libhts0.postrm.debhelper
- chmod 644 debian/libhts0/DEBIAN/shlibs
- chown 0:0 debian/libhts0/DEBIAN/shlibs
- dpkg-gensymbols -plibhts0 -Idebian/libhts0.symbols -Pdebian/libhts0 "-edebian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1\
+ rm -f debian/libhts1/DEBIAN/shlibs
+ install -d debian/libhts1/DEBIAN
+ echo 'libhts 1 libhts1' >>debian/libhts1/DEBIAN/shlibs
+ echo "# Automatically added by dh_makeshlibs">> debian/libhts1.postinst.debhelper
+ sed "" /usr/share/debhelper/autoscripts/postinst-makeshlibs >> debian/libhts1.postinst.debhelper
+ echo '# End automatically added section' >> debian/libhts1.postinst.debhelper
+ echo "# Automatically added by dh_makeshlibs">> debian/libhts1.postrm.debhelper
+ sed "" /usr/share/debhelper/autoscripts/postrm-makeshlibs >> debian/libhts1.postrm.debhelper
+ echo '# End automatically added section' >> debian/libhts1.postrm.debhelper
+ chmod 644 debian/libhts1/DEBIAN/shlibs
+ chown 0:0 debian/libhts1/DEBIAN/shlibs
+ dpkg-gensymbols -plibhts1 -Idebian/libhts1.symbols -Pdebian/libhts1 "-edebian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.0-1\
"
- (grep -s -v misc:Pre-Depends debian/libhts0.substvars; echo misc:Pre-Depends=multiarch-support) > debian/libhts0.substvars.new
- mv debian/libhts0.substvars.new debian/libhts0.substvars
+ (grep -s -v misc:Pre-Depends debian/libhts1.substvars; echo misc:Pre-Depends=multiarch-support) > debian/libhts1.substvars.new
+ mv debian/libhts1.substvars.new debian/libhts1.substvars
rm -f debian/libhts-dev/DEBIAN/shlibs
rm -f debian/htslib-test/DEBIAN/shlibs
+ rm -f debian/tabix/DEBIAN/shlibs
dh_shlibdeps
- dpkg-shlibdeps -Tdebian/libhts0.substvars debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1
-dpkg-shlibdeps: warning: symbol log used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol lgamma used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol pthread_create used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol pthread_join used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol exp used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol pthread_kill used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.0.1 found in none of the libraries
+ dpkg-shlibdeps -Tdebian/libhts1.substvars debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.0-1
install -o 0 -g 0 -d debian/libhts-dev/DEBIAN
install -o 0 -g 0 -d debian/htslib-test/DEBIAN
+ install -o 0 -g 0 -d debian/tabix/DEBIAN
+ dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip
dh_installdeb
printf '#!/bin/sh
set -e
-' > debian/libhts0/DEBIAN/postinst
- cat debian/libhts0.postinst.debhelper >> debian/libhts0/DEBIAN/postinst
- chown 0:0 debian/libhts0/DEBIAN/postinst
- chmod 755 debian/libhts0/DEBIAN/postinst
+' > debian/libhts1/DEBIAN/postinst
+ cat debian/libhts1.postinst.debhelper >> debian/libhts1/DEBIAN/postinst
+ chown 0:0 debian/libhts1/DEBIAN/postinst
+ chmod 755 debian/libhts1/DEBIAN/postinst
printf '#!/bin/sh
set -e
-' > debian/libhts0/DEBIAN/postrm
- cat debian/libhts0.postrm.debhelper >> debian/libhts0/DEBIAN/postrm
- chown 0:0 debian/libhts0/DEBIAN/postrm
- chmod 755 debian/libhts0/DEBIAN/postrm
+' > debian/libhts1/DEBIAN/postrm
+ cat debian/libhts1.postrm.debhelper >> debian/libhts1/DEBIAN/postrm
+ chown 0:0 debian/libhts1/DEBIAN/postrm
+ chmod 755 debian/libhts1/DEBIAN/postrm
dh_gencontrol
- echo misc:Depends= >> debian/libhts0.substvars
- dpkg-gencontrol -plibhts0 -ldebian/changelog -Tdebian/libhts0.substvars -Pdebian/libhts0
+ echo misc:Depends= >> debian/libhts1.substvars
+ dpkg-gencontrol -plibhts1 -ldebian/changelog -Tdebian/libhts1.substvars -Pdebian/libhts1
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: package libhts0: unused substitution variable ${misc:Pre-Depends}
- chmod 644 debian/libhts0/DEBIAN/control
- chown 0:0 debian/libhts0/DEBIAN/control
+ chmod 644 debian/libhts1/DEBIAN/control
+ chown 0:0 debian/libhts1/DEBIAN/control
echo misc:Depends= >> debian/libhts-dev.substvars
dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -Pdebian/libhts-dev
-dpkg-gencontrol: warning: Depends field of package libhts-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 644 debian/libhts-dev/DEBIAN/control
chown 0:0 debian/libhts-dev/DEBIAN/control
echo misc:Depends= >> debian/htslib-test.substvars
dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -Pdebian/htslib-test
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: package htslib-test: unused substitution variable ${perl:Depends}
chmod 644 debian/htslib-test/DEBIAN/control
chown 0:0 debian/htslib-test/DEBIAN/control
+ echo misc:Depends= >> debian/tabix.substvars
+ dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+ chmod 644 debian/tabix/DEBIAN/control
+ chown 0:0 debian/tabix/DEBIAN/control
dh_md5sums
- (cd debian/libhts0 >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
- chmod 644 debian/libhts0/DEBIAN/md5sums
- chown 0:0 debian/libhts0/DEBIAN/md5sums
+ (cd debian/libhts1 >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/libhts1/DEBIAN/md5sums
+ chown 0:0 debian/libhts1/DEBIAN/md5sums
(cd debian/libhts-dev >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 644 debian/libhts-dev/DEBIAN/md5sums
chown 0:0 debian/libhts-dev/DEBIAN/md5sums
(cd debian/htslib-test >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 644 debian/htslib-test/DEBIAN/md5sums
chown 0:0 debian/htslib-test/DEBIAN/md5sums
+ (cd debian/tabix >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/tabix/DEBIAN/md5sums
+ chown 0:0 debian/tabix/DEBIAN/md5sums
dh_builddeb
- dpkg-deb --build debian/libhts0 ..
-dpkg-deb: building package `libhts0' in `../libhts0_0.2.0~rc3-1_amd64.deb'.
+ dpkg-deb --build debian/libhts1 ..
+dpkg-deb: building package `libhts1' in `../libhts1_1.0-1_amd64.deb'.
dpkg-deb --build debian/libhts-dev ..
-dpkg-deb: building package `libhts-dev' in `../libhts-dev_0.2.0~rc3-1_amd64.deb'.
+dpkg-deb: building package `libhts-dev' in `../libhts-dev_1.0-1_amd64.deb'.
dpkg-deb --build debian/htslib-test ..
-dpkg-deb: building package `htslib-test' in `../htslib-test_0.2.0~rc3-1_all.deb'.
- dpkg-genchanges >../htslib_0.2.0~rc3-1_amd64.changes
+dpkg-deb: building package `htslib-test' in `../htslib-test_1.0-1_all.deb'.
+ dpkg-deb --build debian/tabix ..
+dpkg-deb: building package `tabix' in `../tabix_1.0-1_amd64.deb'.
+ dpkg-genchanges >../htslib_1.0-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build htslib-0.2.0~rc3
+ dpkg-source --after-build htslib-1.0
+dpkg-source: info: using options from htslib-1.0/debian/source/options: --single-debian-patch
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20131116-1538
+Build finished at 20140818-2051
Finished
────────
@@ -1183,7 +1056,7 @@ lintian
Merged Build-Depends: lintian
Filtered Build-Depends: lintian
-dpkg-deb: building package `sbuild-build-depends-lintian-dummy' in `/«BUILDDIR»/resolver-dVjKkY/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-lintian-dummy' in `/«BUILDDIR»/resolver-VoFDgK/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
OK
Reading package lists...
@@ -1206,7 +1079,7 @@ The following extra packages will be installed:
libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
patchutils t1utils
Suggested packages:
- libwww-perl binutils-multiarch libtext-template-perl
+ ca-certificates libwww-perl binutils-multiarch libyaml-perl
Recommended packages:
libauthen-sasl-perl libhtml-parser-perl libhtml-template-perl
libxml-simple-perl libperlio-gzip-perl ifupdown
@@ -1222,118 +1095,151 @@ The following NEW packages will be installed:
patchutils sbuild-build-depends-lintian-dummy t1utils
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/3481 kB of archives.
-After this operation, 11.1 MB of additional disk space will be used.
+Need to get 0 B/3671 kB of archives.
+After this operation, 11.9 MB of additional disk space will be used.
Selecting previously unselected package libssl1.0.0:amd64.
-(Reading database ... 12543 files and directories currently installed.)
-Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1e-4_amd64.deb) ...
+(Reading database ... 12617 files and directories currently installed.)
+Preparing to unpack .../libssl1.0.0_1.0.1i-2_amd64.deb ...
+Unpacking libssl1.0.0:amd64 (1.0.1i-2) ...
Selecting previously unselected package netbase.
-Unpacking netbase (from .../archives/netbase_5.1_all.deb) ...
+Preparing to unpack .../archives/netbase_5.2_all.deb ...
+Unpacking netbase (5.2) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.57-1_amd64.deb) ...
+Preparing to unpack .../diffstat_1.58-1_amd64.deb ...
+Unpacking diffstat (1.58-1) ...
Selecting previously unselected package hardening-includes.
-Unpacking hardening-includes (from .../hardening-includes_2.4_all.deb) ...
+Preparing to unpack .../hardening-includes_2.5_all.deb ...
+Unpacking hardening-includes (2.5) ...
Selecting previously unselected package libapt-pkg-perl.
-Unpacking libapt-pkg-perl (from .../libapt-pkg-perl_0.1.29+b1_amd64.deb) ...
+Preparing to unpack .../libapt-pkg-perl_0.1.29+b2_amd64.deb ...
+Unpacking libapt-pkg-perl (0.1.29+b2) ...
Selecting previously unselected package libarchive-zip-perl.
-Unpacking libarchive-zip-perl (from .../libarchive-zip-perl_1.30-7_all.deb) ...
+Preparing to unpack .../libarchive-zip-perl_1.37-2_all.deb ...
+Unpacking libarchive-zip-perl (1.37-2) ...
Selecting previously unselected package libsub-name-perl.
-Unpacking libsub-name-perl (from .../libsub-name-perl_0.05-1+b3_amd64.deb) ...
+Preparing to unpack .../libsub-name-perl_0.07-1+b1_amd64.deb ...
+Unpacking libsub-name-perl (0.07-1+b1) ...
Selecting previously unselected package libclass-accessor-perl.
-Unpacking libclass-accessor-perl (from .../libclass-accessor-perl_0.34-1_all.deb) ...
+Preparing to unpack .../libclass-accessor-perl_0.34-1_all.deb ...
+Unpacking libclass-accessor-perl (0.34-1) ...
Selecting previously unselected package libclone-perl.
-Unpacking libclone-perl (from .../libclone-perl_0.35-1_amd64.deb) ...
+Preparing to unpack .../libclone-perl_0.37-1+b1_amd64.deb ...
+Unpacking libclone-perl (0.37-1+b1) ...
Selecting previously unselected package libdigest-hmac-perl.
-Unpacking libdigest-hmac-perl (from .../libdigest-hmac-perl_1.03+dfsg-1_all.deb) ...
+Preparing to unpack .../libdigest-hmac-perl_1.03+dfsg-1_all.deb ...
+Unpacking libdigest-hmac-perl (1.03+dfsg-1) ...
Selecting previously unselected package libnet-ssleay-perl.
-Unpacking libnet-ssleay-perl (from .../libnet-ssleay-perl_1.55-1+b2_amd64.deb) ...
+Preparing to unpack .../libnet-ssleay-perl_1.65-1+b1_amd64.deb ...
+Unpacking libnet-ssleay-perl (1.65-1+b1) ...
Selecting previously unselected package libio-socket-ssl-perl.
-Unpacking libio-socket-ssl-perl (from .../libio-socket-ssl-perl_1.955-1_all.deb) ...
+Preparing to unpack .../libio-socket-ssl-perl_1.997-2_all.deb ...
+Unpacking libio-socket-ssl-perl (1.997-2) ...
Selecting previously unselected package libnet-smtp-ssl-perl.
-Unpacking libnet-smtp-ssl-perl (from .../libnet-smtp-ssl-perl_1.01-3_all.deb) ...
+Preparing to unpack .../libnet-smtp-ssl-perl_1.01-3_all.deb ...
+Unpacking libnet-smtp-ssl-perl (1.01-3) ...
Selecting previously unselected package libmailtools-perl.
-Unpacking libmailtools-perl (from .../libmailtools-perl_2.12-1_all.deb) ...
-Selecting previously unselected package libnet-ip-perl.
-Unpacking libnet-ip-perl (from .../libnet-ip-perl_1.26-1_all.deb) ...
+Preparing to unpack .../libmailtools-perl_2.12-1_all.deb ...
+Unpacking libmailtools-perl (2.12-1) ...
Selecting previously unselected package libsocket6-perl.
-Unpacking libsocket6-perl (from .../libsocket6-perl_0.23+ds-0+nmu1_amd64.deb) ...
+Preparing to unpack .../libsocket6-perl_0.25-1+b1_amd64.deb ...
+Unpacking libsocket6-perl (0.25-1+b1) ...
Selecting previously unselected package libio-socket-inet6-perl.
-Unpacking libio-socket-inet6-perl (from .../libio-socket-inet6-perl_2.71-1_all.deb) ...
+Preparing to unpack .../libio-socket-inet6-perl_2.72-1_all.deb ...
+Unpacking libio-socket-inet6-perl (2.72-1) ...
+Selecting previously unselected package libnet-ip-perl.
+Preparing to unpack .../libnet-ip-perl_1.26-1_all.deb ...
+Unpacking libnet-ip-perl (1.26-1) ...
Selecting previously unselected package libnet-dns-perl.
-Unpacking libnet-dns-perl (from .../libnet-dns-perl_0.68-1.2_amd64.deb) ...
+Preparing to unpack .../libnet-dns-perl_0.78-1+b1_amd64.deb ...
+Unpacking libnet-dns-perl (0.78-1+b1) ...
Selecting previously unselected package libnet-domain-tld-perl.
-Unpacking libnet-domain-tld-perl (from .../libnet-domain-tld-perl_1.70-1_all.deb) ...
+Preparing to unpack .../libnet-domain-tld-perl_1.72-1_all.deb ...
+Unpacking libnet-domain-tld-perl (1.72-1) ...
Selecting previously unselected package libemail-valid-perl.
-Unpacking libemail-valid-perl (from .../libemail-valid-perl_1.192-1_all.deb) ...
+Preparing to unpack .../libemail-valid-perl_1.194-1_all.deb ...
+Unpacking libemail-valid-perl (1.194-1) ...
Selecting previously unselected package libfile-basedir-perl.
-Unpacking libfile-basedir-perl (from .../libfile-basedir-perl_0.03-1_all.deb) ...
+Preparing to unpack .../libfile-basedir-perl_0.03-1_all.deb ...
+Unpacking libfile-basedir-perl (0.03-1) ...
Selecting previously unselected package libio-pty-perl.
-Unpacking libio-pty-perl (from .../libio-pty-perl_1%3a1.08-1+b3_amd64.deb) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_amd64.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
Selecting previously unselected package libio-string-perl.
-Unpacking libio-string-perl (from .../libio-string-perl_1.08-2_all.deb) ...
+Preparing to unpack .../libio-string-perl_1.08-3_all.deb ...
+Unpacking libio-string-perl (1.08-3) ...
Selecting previously unselected package libipc-run-perl.
-Unpacking libipc-run-perl (from .../libipc-run-perl_0.92-1_all.deb) ...
+Preparing to unpack .../libipc-run-perl_0.92-1_all.deb ...
+Unpacking libipc-run-perl (0.92-1) ...
Selecting previously unselected package liblist-moreutils-perl.
-Unpacking liblist-moreutils-perl (from .../liblist-moreutils-perl_0.33-1+b2_amd64.deb) ...
+Preparing to unpack .../liblist-moreutils-perl_0.33-2+b1_amd64.deb ...
+Unpacking liblist-moreutils-perl (0.33-2+b1) ...
Selecting previously unselected package libparse-debianchangelog-perl.
-Unpacking libparse-debianchangelog-perl (from .../libparse-debianchangelog-perl_1.2.0-1_all.deb) ...
+Preparing to unpack .../libparse-debianchangelog-perl_1.2.0-1_all.deb ...
+Unpacking libparse-debianchangelog-perl (1.2.0-1) ...
Selecting previously unselected package libtext-levenshtein-perl.
-Unpacking libtext-levenshtein-perl (from .../libtext-levenshtein-perl_0.06~01-2_all.deb) ...
+Preparing to unpack .../libtext-levenshtein-perl_0.09-1_all.deb ...
+Unpacking libtext-levenshtein-perl (0.09-1) ...
Selecting previously unselected package liburi-perl.
-Unpacking liburi-perl (from .../liburi-perl_1.60-1_all.deb) ...
+Preparing to unpack .../liburi-perl_1.64-1_all.deb ...
+Unpacking liburi-perl (1.64-1) ...
Selecting previously unselected package patchutils.
-Unpacking patchutils (from .../patchutils_0.3.2-3_amd64.deb) ...
+Preparing to unpack .../patchutils_0.3.3-1_amd64.deb ...
+Unpacking patchutils (0.3.3-1) ...
Selecting previously unselected package t1utils.
-Unpacking t1utils (from .../t1utils_1.37-2_amd64.deb) ...
+Preparing to unpack .../t1utils_1.37-2_amd64.deb ...
+Unpacking t1utils (1.37-2) ...
Selecting previously unselected package lintian.
-Unpacking lintian (from .../lintian_2.5.19_all.deb) ...
+Preparing to unpack .../lintian_2.5.25_all.deb ...
+Unpacking lintian (2.5.25) ...
Selecting previously unselected package sbuild-build-depends-lintian-dummy.
-Unpacking sbuild-build-depends-lintian-dummy (from .../sbuild-build-depends-lintian-dummy.deb) ...
-Processing triggers for man-db ...
+Preparing to unpack .../sbuild-build-depends-lintian-dummy.deb ...
+Unpacking sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Processing triggers for man-db (2.6.7.1-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libssl1.0.0:amd64 (1.0.1e-4) ...
-Setting up netbase (5.1) ...
-Setting up diffstat (1.57-1) ...
-Setting up hardening-includes (2.4) ...
-Setting up libapt-pkg-perl (0.1.29+b1) ...
-Setting up libarchive-zip-perl (1.30-7) ...
-Setting up libsub-name-perl (0.05-1+b3) ...
+Setting up libssl1.0.0:amd64 (1.0.1i-2) ...
+Setting up netbase (5.2) ...
+Setting up diffstat (1.58-1) ...
+Setting up hardening-includes (2.5) ...
+Setting up libapt-pkg-perl (0.1.29+b2) ...
+Setting up libarchive-zip-perl (1.37-2) ...
+Setting up libsub-name-perl (0.07-1+b1) ...
Setting up libclass-accessor-perl (0.34-1) ...
-Setting up libclone-perl (0.35-1) ...
+Setting up libclone-perl (0.37-1+b1) ...
Setting up libdigest-hmac-perl (1.03+dfsg-1) ...
-Setting up libnet-ssleay-perl (1.55-1+b2) ...
-Setting up libio-socket-ssl-perl (1.955-1) ...
+Setting up libnet-ssleay-perl (1.65-1+b1) ...
+Setting up libio-socket-ssl-perl (1.997-2) ...
Setting up libnet-smtp-ssl-perl (1.01-3) ...
Setting up libmailtools-perl (2.12-1) ...
+Setting up libsocket6-perl (0.25-1+b1) ...
+Setting up libio-socket-inet6-perl (2.72-1) ...
Setting up libnet-ip-perl (1.26-1) ...
-Setting up libsocket6-perl (0.23+ds-0+nmu1) ...
-Setting up libio-socket-inet6-perl (2.71-1) ...
-Setting up libnet-dns-perl (0.68-1.2) ...
-Setting up libnet-domain-tld-perl (1.70-1) ...
-Setting up libemail-valid-perl (1.192-1) ...
+Setting up libnet-dns-perl (0.78-1+b1) ...
+Setting up libnet-domain-tld-perl (1.72-1) ...
+Setting up libemail-valid-perl (1.194-1) ...
Setting up libfile-basedir-perl (0.03-1) ...
-Setting up libio-pty-perl (1:1.08-1+b3) ...
-Setting up libio-string-perl (1.08-2) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libio-string-perl (1.08-3) ...
Setting up libipc-run-perl (0.92-1) ...
-Setting up liblist-moreutils-perl (0.33-1+b2) ...
+Setting up liblist-moreutils-perl (0.33-2+b1) ...
Setting up libparse-debianchangelog-perl (1.2.0-1) ...
-Setting up libtext-levenshtein-perl (0.06~01-2) ...
-Setting up liburi-perl (1.60-1) ...
-Setting up patchutils (0.3.2-3) ...
+Setting up libtext-levenshtein-perl (0.09-1) ...
+Setting up liburi-perl (1.64-1) ...
+Setting up patchutils (0.3.3-1) ...
Setting up t1utils (1.37-2) ...
-Setting up lintian (2.5.19) ...
+Setting up lintian (2.5.25) ...
Setting up sbuild-build-depends-lintian-dummy (0.invalid.0) ...
-Processing triggers for libc-bin ...
-W: htslib source: brace-expansion-in-debhelper-config-file debian/libhts-dev.install
-W: htslib source: brace-expansion-in-debhelper-config-file debian/libhts0.install
-I: htslib source: missing-debian-source-format
-P: htslib source: direct-changes-in-diff-but-no-patch-system bgzf.c and 9 more
-W: htslib source: newer-standards-version 3.9.5 (current is 3.9.4)
+Processing triggers for libc-bin (2.19-9) ...
+P: htslib source: debian-watch-may-check-gpg-signature
+P: libhts1: no-upstream-changelog
P: htslib-test: no-upstream-changelog
-W: libhts0: hardening-no-relro usr/lib/x86_64-linux-gnu/libhts.so.0.0.1
-P: libhts0: no-upstream-changelog
+I: htslib-test: extended-description-is-probably-too-short
+P: tabix: no-upstream-changelog
+W: tabix: manpage-has-errors-from-man usr/share/man/man1/tabix.1.gz `R' is a string (producing the registered sign), not a macro.
+I: tabix: hyphen-used-as-minus-sign usr/share/man/man1/tabix.1.gz:124
+I: tabix: hyphen-used-as-minus-sign usr/share/man/man1/tabix.1.gz:126
P: libhts-dev: no-upstream-changelog
-W: libhts-dev: manpage-has-errors-from-man usr/share/man/man5/vcf.5.gz file `<standard input>', around line 15:
+I: libhts-dev: extended-description-is-probably-too-short
+W: libhts-dev: manpage-has-errors-from-man usr/share/man/man5/vcf.5.gz file `<standard input>', around line 39:
I: Lintian run was successful.
@@ -1342,240 +1248,293 @@ I: Lintian run was successful.
└──────────────────────────────────────────────────────────────────────────────┘
-htslib_0.2.0~rc3-1_amd64.changes:
-─────────────────────────────────
+htslib_1.0-1_amd64.changes:
+───────────────────────────
Format: 1.8
-Date: Sat, 16 Nov 2013 15:35:03 +0900
+Date: Sun, 17 Aug 2014 20:12:28 +0900
Source: htslib
-Binary: libhts0 libhts-dev htslib-test
+Binary: libhts1 libhts-dev htslib-test tabix
Architecture: source amd64 all
-Version: 0.2.0~rc3-1
+Version: 1.0-1
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:
+Description:
htslib-test - Test data for HTSlib
libhts-dev - Development files for the HTSlib
- libhts0 - C library for high-throughput sequencing data formats
-Closes: 729282
-Changes:
- htslib (0.2.0~rc3-1) unstable; urgency=low
+ libhts1 - C library for high-throughput sequencing data formats
+ tabix - generic indexer for TAB-delimited genome position files
+Changes:
+ htslib (1.0-1) experimental; urgency=low
.
- * Initial release. (Closes: #729282)
-Checksums-Sha1:
- 8e440416198ca459f60188a2321152af7432ce2f 1153 htslib_0.2.0~rc3-1.dsc
- a34fc68574d10754d9813fdb7ce4dad52da99d05 923352 htslib_0.2.0~rc3.orig.tar.gz
- 336b5f8094a71997a7cbd74d0d1c69f43801449b 10532 htslib_0.2.0~rc3-1.diff.gz
- 68883a6fb26a0c9fc5d057d370eff2c5d795af5d 183826 libhts0_0.2.0~rc3-1_amd64.deb
- 65beede3659386ae4d9df13d15bcb770b77b2112 221284 libhts-dev_0.2.0~rc3-1_amd64.deb
- ac04ef188b27f4aed31836d948d3c1e5afb8d5ec 514106 htslib-test_0.2.0~rc3-1_all.deb
-Checksums-Sha256:
- d7a5f98d93b0468380d439ca52bdcef1dfa990e8057e362d30473c2f0e632606 1153 htslib_0.2.0~rc3-1.dsc
- 5e972ce7048c9b236911cd30e2100f7bfb28e65aa4cc3687a9aaf31d116be3ce 923352 htslib_0.2.0~rc3.orig.tar.gz
- 3575954047af6c97d4500b3eb0b0bf78c327f355804a54844a128bb5391dd1a8 10532 htslib_0.2.0~rc3-1.diff.gz
- ca825bf740968fab20c50d49be6ea446f6dad4cc041638af28e51c48c4b8092b 183826 libhts0_0.2.0~rc3-1_amd64.deb
- 49f8bb3be8c784927e60bc856fbe3004f013f26dfe7b8f06f7e80754c6db4bd2 221284 libhts-dev_0.2.0~rc3-1_amd64.deb
- 7fd8597061206552f31f146276bac59473d2e96fb751c1f6451affdbe7a49f6b 514106 htslib-test_0.2.0~rc3-1_all.deb
-Files:
- e1146c59ebd8de27c5acfe4621fb6720 1153 libs optional htslib_0.2.0~rc3-1.dsc
- 5d055a061e84ae987b25cb72bb4173d6 923352 libs optional htslib_0.2.0~rc3.orig.tar.gz
- e7f26daf824e4fa67171c78cc6ef932b 10532 libs optional htslib_0.2.0~rc3-1.diff.gz
- 136ca39311885c1aeffe2565f9cfcd47 183826 libs optional libhts0_0.2.0~rc3-1_amd64.deb
- bb6e3c45eb785b132025527bd2bdc884 221284 libdevel optional libhts-dev_0.2.0~rc3-1_amd64.deb
- 40e1ca3c045337aad2355198183ead36 514106 libs optional htslib-test_0.2.0~rc3-1_all.deb
+ cc559b8 Merged with upstream's master branch.
+ 74b9d7b Build on the master branch.
+ 04815a7 New major version (libhts0 -> libhts1).
+ 98c18ca Updated symbols file.
+ 22fef0c Install pkgconfig file.
+ 420896b Override PACKAGE_VERSION to avoid tags with a slash in the name.
+ 79b5d4e Use the Debian package version as PACKAGE_VERSION.
+ 72b5c4a Finally use the 3.0 (quilt) format in single-debian-patch mode.
+ d870946 Adjusted substitution variables following dpkg's warnings.
+ 9469458 Removed debug command accidentally introduced.
+ 8c7f7d4 Replace the old tabix package from the tabix source package.
+Checksums-Sha1:
+ 1851bed43f7a2b7655dc3323e79d8f8183266ba1 1204 htslib_1.0-1.dsc
+ 3eca8a7e919782def2478347b5824bab15ca2d10 956351 htslib_1.0.orig.tar.gz
+ ad6c9b6e54725071e4ba82ef616ec1b0f04a31ca 7296 htslib_1.0-1.debian.tar.xz
+ 58e45a3d2e0cf52f3081e7dbc478755c6b982e35 203538 libhts1_1.0-1_amd64.deb
+ 37e40e3532d70f851ec20b87f5cbe6bca5bfce5d 248802 libhts-dev_1.0-1_amd64.deb
+ 848836bfa686c6ea1a883e0e4e1363b55c141627 515934 htslib-test_1.0-1_all.deb
+ 4bcc64ace3cf22c093a3c88b895ec816d00e6380 189596 tabix_1.0-1_amd64.deb
+Checksums-Sha256:
+ 9041191a572133cfbdda78127d18c541488c93bcc91c0afe3e0f6f81c7a3b138 1204 htslib_1.0-1.dsc
+ 93ba8de2bc35040f17ca2fbfed3d161fd278f394e82cdfe443336948311b88a8 956351 htslib_1.0.orig.tar.gz
+ 207c357a597bb3871c93c17e84a169227d164a3ec14defcc170fe8e0517f8e1a 7296 htslib_1.0-1.debian.tar.xz
+ 9cb8388234c8f712a92e29da2ede573703bc1dbc061baf57b6d6085e10db8ed6 203538 libhts1_1.0-1_amd64.deb
+ 3a3a026fd431c6d2456f3ee7c144976bd2283d41b19f3e91c2391cce2ea7a876 248802 libhts-dev_1.0-1_amd64.deb
+ a5e218f10bdbd769dae4d8e03c3a9182c41c200af3b3b1d9005cf54614c31112 515934 htslib-test_1.0-1_all.deb
+ 2b272f5b5411d356b60794f89bf2d353a3e4d2e5ec07aecac6666eb871fe67cd 189596 tabix_1.0-1_amd64.deb
+Files:
+ 52dd57f6e124c76204d32fa0d7267bf5 203538 libs optional libhts1_1.0-1_amd64.deb
+ dc3e7a5a49b89249ddd4d53c0f84511c 248802 libdevel optional libhts-dev_1.0-1_amd64.deb
+ 94fe486b55f89696f622768aba48f838 515934 science optional htslib-test_1.0-1_all.deb
+ 454fbd54cb02e47e6dd2f0d929ab7824 189596 science optional tabix_1.0-1_amd64.deb
+ a634c6d47e2664982b423081707342db 1204 science optional htslib_1.0-1.dsc
+ 3c7ffe5ffa81fea55b4c33132ae77424 956351 science optional htslib_1.0.orig.tar.gz
+ fe23052ac3b5c82f493f343aea0a580a 7296 science optional htslib_1.0-1.debian.tar.xz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-libhts0_0.2.0~rc3-1_amd64.deb
-─────────────────────────────
+libhts1_1.0-1_amd64.deb
+───────────────────────
new debian package, version 2.0.
- size 183826 bytes: control archive=3637 bytes.
- 878 bytes, 22 lines control
+ size 203538 bytes: control archive=4377 bytes.
+ 979 bytes, 22 lines control
217 bytes, 3 lines md5sums
135 bytes, 7 lines * postinst #!/bin/sh
132 bytes, 7 lines * postrm #!/bin/sh
17 bytes, 1 lines shlibs
- 15859 bytes, 507 lines symbols
- Package: libhts0
+ 13474 bytes, 529 lines symbols
+ Package: libhts1
Source: htslib
- Version: 0.2.0~rc3-1
+ Version: 1.0-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 508
- Depends: libc6 (>= 2.15), zlib1g (>= 1:1.2.2)
+ Installed-Size: 543
+ Pre-Depends: multiarch-support
+ Depends: libc6 (>= 2.15), zlib1g (>= 1:1.2.0.2)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/samtools/htslib
Description: C library for high-throughput sequencing data formats
- HTSlib is a unified C library for accessing common file formats, such as SAM
- (Sequence Alignment/Map) and VCF (Variant Call Format), used for nucleic acid
- sequence data obtained by high-throughput sequencing.
- .
- HTSlib implements a generalized BAM (binary SAM) index. The HTSlib file
- reader first looks for the new index and then for the old if the new index is
- absent.
+ HTSlib is an implementation of a unified C library for accessing common file
+ formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
+ Format), used for high-throughput sequencing data, and is the core library
+ used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
+ compatible with gcc, g++ and clang.
.
- HTSlib is still experimental. It has not been tested on large-scale real
- data. Some useful APIs are missing.
-
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/doc/libhts0/
--rw-r--r-- root/root 7175 2013-11-16 15:36 ./usr/share/doc/libhts0/copyright
--rw-r--r-- root/root 160 2013-11-16 15:36 ./usr/share/doc/libhts0/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/lib/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/lib/x86_64-linux-gnu/
--rw-r--r-- root/root 463656 2013-11-16 15:37 ./usr/lib/x86_64-linux-gnu/libhts.so.0.0.1
-lrwxrwxrwx root/root 0 2013-11-16 15:37 ./usr/lib/x86_64-linux-gnu/libhts.so.0 -> libhts.so.0.0.1
-
-
-libhts-dev_0.2.0~rc3-1_amd64.deb
-────────────────────────────────
+ HTSlib implements a generalized BAM (binary SAM) index, with file extension
+ ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
+ new index and then for the old if the new index is absent.
+
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/doc/libhts1/
+-rw-r--r-- root/root 7175 2014-08-16 18:30 ./usr/share/doc/libhts1/copyright
+-rw-r--r-- root/root 561 2014-08-18 20:47 ./usr/share/doc/libhts1/changelog.Debian.gz
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/lib/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/lib/x86_64-linux-gnu/
+-rw-r--r-- root/root 501280 2014-08-18 20:50 ./usr/lib/x86_64-linux-gnu/libhts.so.1.0-1
+lrwxrwxrwx root/root 0 2014-08-18 20:50 ./usr/lib/x86_64-linux-gnu/libhts.so.1 -> libhts.so.1.0-1
+
+
+libhts-dev_1.0-1_amd64.deb
+──────────────────────────
new debian package, version 2.0.
- size 221284 bytes: control archive=1304 bytes.
- 661 bytes, 18 lines control
- 1517 bytes, 24 lines md5sums
+ size 248802 bytes: control archive=1306 bytes.
+ 449 bytes, 14 lines control
+ 1667 bytes, 26 lines md5sums
Package: libhts-dev
Source: htslib
- Version: 0.2.0~rc3-1
+ Version: 1.0-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 840
- Depends: libhts0 (= 0.2.0~rc3-1)
+ Installed-Size: 944
+ Depends: libhts1 (= 1.0-1)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/samtools/htslib
Description: Development files for the HTSlib
- HTSlib is a unified C library for accessing common file formats, such as SAM
- (Sequence Alignment/Map) and VCF (Variant Call Format), used for nucleic acid
- sequence data obtained by high-throughput sequencing.
- .
- This package contains development files: headers, static library, manual pages,
- etc.
-
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/man/man5/
--rw-r--r-- root/root 885 2013-11-16 15:37 ./usr/share/man/man5/sam.5.gz
--rw-r--r-- root/root 1429 2013-11-16 15:37 ./usr/share/man/man5/faidx.5.gz
--rw-r--r-- root/root 1197 2013-11-16 15:37 ./usr/share/man/man5/vcf.5.gz
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/doc/libhts-dev/
--rw-r--r-- root/root 7175 2013-11-16 15:36 ./usr/share/doc/libhts-dev/copyright
--rw-r--r-- root/root 160 2013-11-16 15:36 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/include/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/include/htslib/
--rw-r--r-- root/root 1431 2013-10-28 22:03 ./usr/include/htslib/kfunc.h
--rw-r--r-- root/root 1612 2013-10-28 22:03 ./usr/include/htslib/knetfile.h
--rw-r--r-- root/root 8896 2013-10-28 22:03 ./usr/include/htslib/sam.h
--rw-r--r-- root/root 9607 2013-11-16 15:36 ./usr/include/htslib/bgzf.h
--rw-r--r-- root/root 1493 2013-10-28 22:03 ./usr/include/htslib/tbx.h
--rw-r--r-- root/root 3615 2013-10-28 22:03 ./usr/include/htslib/faidx.h
--rw-r--r-- root/root 8934 2013-10-28 22:03 ./usr/include/htslib/kseq.h
--rw-r--r-- root/root 346 2013-10-28 22:03 ./usr/include/htslib/vcf_sweep.h
--rw-r--r-- root/root 4640 2013-10-28 22:03 ./usr/include/htslib/klist.h
--rw-r--r-- root/root 7280 2013-11-16 15:36 ./usr/include/htslib/hts.h
--rw-r--r-- root/root 21224 2013-10-28 22:03 ./usr/include/htslib/khash.h
--rw-r--r-- root/root 4151 2013-10-28 22:03 ./usr/include/htslib/razf.h
--rw-r--r-- root/root 9112 2013-10-28 22:03 ./usr/include/htslib/synced_bcf_reader.h
--rw-r--r-- root/root 2312 2013-10-28 22:03 ./usr/include/htslib/kstdint.h
--rw-r--r-- root/root 2875 2013-11-16 15:36 ./usr/include/htslib/vcfutils.h
--rw-r--r-- root/root 6332 2013-10-28 22:03 ./usr/include/htslib/kstring.h
--rw-r--r-- root/root 26737 2013-10-28 22:03 ./usr/include/htslib/vcf.h
--rw-r--r-- root/root 10125 2013-10-28 22:03 ./usr/include/htslib/ksort.h
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/lib/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/lib/x86_64-linux-gnu/
--rw-r--r-- root/root 668682 2013-11-16 15:37 ./usr/lib/x86_64-linux-gnu/libhts.a
-lrwxrwxrwx root/root 0 2013-11-16 15:37 ./usr/lib/x86_64-linux-gnu/libhts.so -> libhts.so.0.0.1
-
-
-htslib-test_0.2.0~rc3-1_all.deb
-───────────────────────────────
+ This package contains development files for the HTSlib: headers, static
+ library, manual pages, etc.
+
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/man/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/man/man5/
+-rw-r--r-- root/root 1535 2014-08-18 20:50 ./usr/share/man/man5/sam.5.gz
+-rw-r--r-- root/root 2081 2014-08-18 20:50 ./usr/share/man/man5/faidx.5.gz
+-rw-r--r-- root/root 1854 2014-08-18 20:50 ./usr/share/man/man5/vcf.5.gz
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/doc/libhts-dev/
+-rw-r--r-- root/root 7175 2014-08-16 18:30 ./usr/share/doc/libhts-dev/copyright
+-rw-r--r-- root/root 561 2014-08-18 20:47 ./usr/share/doc/libhts-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/include/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/include/htslib/
+-rw-r--r-- root/root 2647 2014-08-15 19:04 ./usr/include/htslib/kfunc.h
+-rw-r--r-- root/root 2828 2014-08-15 19:04 ./usr/include/htslib/knetfile.h
+-rw-r--r-- root/root 15120 2014-08-15 19:04 ./usr/include/htslib/sam.h
+-rw-r--r-- root/root 10450 2014-08-15 19:04 ./usr/include/htslib/bgzf.h
+-rw-r--r-- root/root 2747 2014-08-15 19:04 ./usr/include/htslib/tbx.h
+-rw-r--r-- root/root 3637 2014-08-15 19:04 ./usr/include/htslib/khash_str2int.h
+-rw-r--r-- root/root 4101 2014-08-15 19:04 ./usr/include/htslib/faidx.h
+-rw-r--r-- root/root 8934 2014-08-15 19:04 ./usr/include/htslib/kseq.h
+-rw-r--r-- root/root 1517 2014-08-15 19:04 ./usr/include/htslib/vcf_sweep.h
+-rw-r--r-- root/root 4651 2014-08-15 19:04 ./usr/include/htslib/klist.h
+-rw-r--r-- root/root 6558 2014-08-15 19:04 ./usr/include/htslib/hfile.h
+-rw-r--r-- root/root 10673 2014-08-15 19:04 ./usr/include/htslib/hts.h
+-rw-r--r-- root/root 21224 2014-08-15 19:04 ./usr/include/htslib/khash.h
+-rw-r--r-- root/root 12203 2014-08-15 19:04 ./usr/include/htslib/synced_bcf_reader.h
+-rw-r--r-- root/root 1721 2014-08-15 19:04 ./usr/include/htslib/hts_defs.h
+-rw-r--r-- root/root 3988 2014-08-15 19:04 ./usr/include/htslib/vcfutils.h
+-rw-r--r-- root/root 6657 2014-08-15 19:04 ./usr/include/htslib/kstring.h
+-rw-r--r-- root/root 37811 2014-08-15 19:04 ./usr/include/htslib/vcf.h
+-rw-r--r-- root/root 10125 2014-08-15 19:04 ./usr/include/htslib/ksort.h
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/lib/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/lib/x86_64-linux-gnu/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/lib/x86_64-linux-gnu/pkgconfig/
+-rw-r--r-- root/root 270 2014-08-18 20:50 ./usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc
+-rw-r--r-- root/root 732262 2014-08-18 20:50 ./usr/lib/x86_64-linux-gnu/libhts.a
+lrwxrwxrwx root/root 0 2014-08-18 20:50 ./usr/lib/x86_64-linux-gnu/libhts.so -> libhts.so.1.0-1
+
+
+htslib-test_1.0-1_all.deb
+─────────────────────────
new debian package, version 2.0.
- size 514106 bytes: control archive=1790 bytes.
- 570 bytes, 15 lines control
- 3099 bytes, 45 lines md5sums
+ size 515934 bytes: control archive=1774 bytes.
+ 366 bytes, 12 lines control
+ 3161 bytes, 46 lines md5sums
Package: htslib-test
Source: htslib
- Version: 0.2.0~rc3-1
+ Version: 1.0-1
Architecture: all
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4103
- Section: libs
+ Installed-Size: 4122
+ Depends: perl
+ Section: science
Priority: optional
Homepage: https://github.com/samtools/htslib
Description: Test data for HTSlib
- HTSlib is a unified C library for accessing common file formats, such as SAM
- (Sequence Alignment/Map) and VCF (Variant Call Format), used for nucleic acid
- sequence data obtained by high-throughput sequencing.
- .
This package contains test files and scripts for the HTSlib.
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/doc/htslib-test/
--rw-r--r-- root/root 7175 2013-11-16 15:36 ./usr/share/doc/htslib-test/copyright
--rw-r--r-- root/root 160 2013-11-16 15:36 ./usr/share/doc/htslib-test/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-11-16 15:37 ./usr/share/htslib-test/
--rw-r--r-- root/root 230 2013-10-28 22:03 ./usr/share/htslib-test/ce.fa.fai
--rw-r--r-- root/root 15 2013-10-28 22:03 ./usr/share/htslib-test/c1.fa
--rw-r--r-- root/root 1287 2013-10-28 22:03 ./usr/share/htslib-test/test-vcf-api.out
--rw-r--r-- root/root 517 2013-10-28 22:03 ./usr/share/htslib-test/xx#rg.sam
--rw-r--r-- root/root 267 2013-10-28 22:03 ./usr/share/htslib-test/xx#triplet.sam
--rw-r--r-- root/root 14 2013-10-28 22:03 ./usr/share/htslib-test/c1.fa.fai
--rw-r--r-- root/root 1889 2013-10-28 22:03 ./usr/share/htslib-test/ce#5.sam
--rw-r--r-- root/root 320 2013-10-28 22:03 ./usr/share/htslib-test/xx#unsorted.sam
--rw-r--r-- root/root 29 2013-10-28 22:03 ./usr/share/htslib-test/aux.fa
--rw-r--r-- root/root 1646 2013-10-28 22:03 ./usr/share/htslib-test/ce#tag_padded.sam
--rw-r--r-- root/root 0 2013-10-28 22:03 ./usr/share/htslib-test/xx#blank.sam
--rw-r--r-- root/root 342 2013-10-28 22:03 ./usr/share/htslib-test/ce#1.sam
--rw-r--r-- root/root 5270 2013-10-28 22:03 ./usr/share/htslib-test/hfile.c
--rw-r--r-- root/root 916 2013-10-28 22:03 ./usr/share/htslib-test/fieldarith.sam
--rw-r--r-- root/root 2769 2013-10-28 22:03 ./usr/share/htslib-test/ce#unmap1.sam
--rw-r--r-- root/root 5536 2013-10-28 22:03 ./usr/share/htslib-test/test-vcf-api.c
--rw-r--r-- root/root 2615 2013-10-28 22:03 ./usr/share/htslib-test/test-vcf-sweep.c
--rw-r--r-- root/root 51 2013-10-28 22:03 ./usr/share/htslib-test/xx.fa
--rwxr-xr-x root/root 2922 2013-10-28 22:03 ./usr/share/htslib-test/compare_sam.pl
--rw-r--r-- root/root 727 2013-10-28 22:03 ./usr/share/htslib-test/aux#aux.sam
--rw-r--r-- root/root 2147245 2013-10-28 22:03 ./usr/share/htslib-test/ce#large_seq.sam
--rw-r--r-- root/root 388 2013-10-28 22:03 ./usr/share/htslib-test/c1#pad1.sam
--rw-r--r-- root/root 1634 2013-10-28 22:03 ./usr/share/htslib-test/ce#tag_depadded.sam
--rw-r--r-- root/root 18 2013-10-28 22:03 ./usr/share/htslib-test/aux.fa.fai
--rw-r--r-- root/root 651 2013-10-28 22:03 ./usr/share/htslib-test/xx#large_aux2.sam
--rw-r--r-- root/root 905485 2013-10-28 22:03 ./usr/share/htslib-test/xx#large_aux.sam
--rw-r--r-- root/root 527 2013-10-28 22:03 ./usr/share/htslib-test/c1#pad2.sam
--rw-r--r-- root/root 1060702 2013-10-28 22:03 ./usr/share/htslib-test/ce.fa
--rw-r--r-- root/root 1853 2013-10-28 22:03 ./usr/share/htslib-test/ce#5b.sam
--rw-r--r-- root/root 148 2013-10-28 22:03 ./usr/share/htslib-test/c1#bounds.sam
--rw-r--r-- root/root 5547 2013-10-28 22:03 ./usr/share/htslib-test/ce#unmap2.sam
--rw-r--r-- root/root 304 2013-10-28 22:03 ./usr/share/htslib-test/xx#pair.sam
--rwxr-xr-x root/root 5086 2013-10-28 22:03 ./usr/share/htslib-test/test.pl
--rw-r--r-- root/root 337 2013-10-28 22:03 ./usr/share/htslib-test/c1#clip.sam
--rw-r--r-- root/root 254 2013-10-28 22:03 ./usr/share/htslib-test/xx#minimal.sam
--rw-r--r-- root/root 2577 2013-10-28 22:03 ./usr/share/htslib-test/test_view.c
--rw-r--r-- root/root 646 2013-10-28 22:03 ./usr/share/htslib-test/ce#2.sam
--rwxr-xr-x root/root 1143 2013-10-28 22:03 ./usr/share/htslib-test/test_view.pl
--rw-r--r-- root/root 29 2013-10-28 22:03 ./usr/share/htslib-test/xx.fa.fai
--rw-r--r-- root/root 1126 2013-10-28 22:03 ./usr/share/htslib-test/fieldarith.c
--rw-r--r-- root/root 1325 2013-10-28 22:03 ./usr/share/htslib-test/ce#unmap.sam
--rw-r--r-- root/root 92 2013-10-28 22:03 ./usr/share/htslib-test/test-vcf-sweep.out
--rw-r--r-- root/root 665 2013-10-28 22:03 ./usr/share/htslib-test/c1#pad3.sam
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/doc/htslib-test/
+-rw-r--r-- root/root 7175 2014-08-16 18:30 ./usr/share/doc/htslib-test/copyright
+-rw-r--r-- root/root 561 2014-08-18 20:47 ./usr/share/doc/htslib-test/changelog.Debian.gz
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/htslib-test/
+-rw-r--r-- root/root 230 2014-08-15 19:04 ./usr/share/htslib-test/ce.fa.fai
+-rw-r--r-- root/root 15 2014-08-15 19:04 ./usr/share/htslib-test/c1.fa
+-rw-r--r-- root/root 1936 2014-08-15 19:04 ./usr/share/htslib-test/test-vcf-api.out
+-rw-r--r-- root/root 517 2014-08-15 19:04 ./usr/share/htslib-test/xx#rg.sam
+-rw-r--r-- root/root 267 2014-08-15 19:04 ./usr/share/htslib-test/xx#triplet.sam
+-rw-r--r-- root/root 14 2014-08-15 19:04 ./usr/share/htslib-test/c1.fa.fai
+-rw-r--r-- root/root 1889 2014-08-15 19:04 ./usr/share/htslib-test/ce#5.sam
+-rw-r--r-- root/root 320 2014-08-15 19:04 ./usr/share/htslib-test/xx#unsorted.sam
+-rw-r--r-- root/root 29 2014-08-15 19:04 ./usr/share/htslib-test/aux.fa
+-rw-r--r-- root/root 1646 2014-08-15 19:04 ./usr/share/htslib-test/ce#tag_padded.sam
+-rw-r--r-- root/root 0 2014-08-15 19:04 ./usr/share/htslib-test/xx#blank.sam
+-rw-r--r-- root/root 342 2014-08-15 19:04 ./usr/share/htslib-test/ce#1.sam
+-rw-r--r-- root/root 6824 2014-08-15 19:04 ./usr/share/htslib-test/hfile.c
+-rw-r--r-- root/root 916 2014-08-15 19:04 ./usr/share/htslib-test/fieldarith.sam
+-rw-r--r-- root/root 2769 2014-08-15 19:04 ./usr/share/htslib-test/ce#unmap1.sam
+-rw-r--r-- root/root 8946 2014-08-15 19:04 ./usr/share/htslib-test/test-vcf-api.c
+-rw-r--r-- root/root 3802 2014-08-15 19:04 ./usr/share/htslib-test/test-vcf-sweep.c
+-rw-r--r-- root/root 51 2014-08-15 19:04 ./usr/share/htslib-test/xx.fa
+-rwxr-xr-x root/root 4351 2014-08-15 19:04 ./usr/share/htslib-test/compare_sam.pl
+-rw-r--r-- root/root 727 2014-08-15 19:04 ./usr/share/htslib-test/aux#aux.sam
+-rw-r--r-- root/root 2147245 2014-08-15 19:04 ./usr/share/htslib-test/ce#large_seq.sam
+-rw-r--r-- root/root 388 2014-08-15 19:04 ./usr/share/htslib-test/c1#pad1.sam
+-rw-r--r-- root/root 1634 2014-08-15 19:04 ./usr/share/htslib-test/ce#tag_depadded.sam
+-rw-r--r-- root/root 18 2014-08-15 19:04 ./usr/share/htslib-test/aux.fa.fai
+-rw-r--r-- root/root 651 2014-08-15 19:04 ./usr/share/htslib-test/xx#large_aux2.sam
+-rw-r--r-- root/root 905485 2014-08-15 19:04 ./usr/share/htslib-test/xx#large_aux.sam
+-rw-r--r-- root/root 527 2014-08-15 19:04 ./usr/share/htslib-test/c1#pad2.sam
+-rw-r--r-- root/root 1060702 2014-08-15 19:04 ./usr/share/htslib-test/ce.fa
+-rw-r--r-- root/root 1853 2014-08-15 19:04 ./usr/share/htslib-test/ce#5b.sam
+-rw-r--r-- root/root 148 2014-08-15 19:04 ./usr/share/htslib-test/c1#bounds.sam
+-rw-r--r-- root/root 5547 2014-08-15 19:04 ./usr/share/htslib-test/ce#unmap2.sam
+-rw-r--r-- root/root 304 2014-08-15 19:04 ./usr/share/htslib-test/xx#pair.sam
+-rwxr-xr-x root/root 6226 2014-08-15 19:04 ./usr/share/htslib-test/test.pl
+-rw-r--r-- root/root 337 2014-08-15 19:04 ./usr/share/htslib-test/c1#clip.sam
+-rw-r--r-- root/root 254 2014-08-15 19:04 ./usr/share/htslib-test/xx#minimal.sam
+-rw-r--r-- root/root 4830 2014-08-15 19:04 ./usr/share/htslib-test/test_view.c
+-rw-r--r-- root/root 646 2014-08-15 19:04 ./usr/share/htslib-test/ce#2.sam
+-rwxr-xr-x root/root 2329 2014-08-15 19:04 ./usr/share/htslib-test/test_view.pl
+-rw-r--r-- root/root 4751 2014-08-15 19:04 ./usr/share/htslib-test/sam.c
+-rw-r--r-- root/root 29 2014-08-15 19:04 ./usr/share/htslib-test/xx.fa.fai
+-rw-r--r-- root/root 2409 2014-08-15 19:04 ./usr/share/htslib-test/fieldarith.c
+-rw-r--r-- root/root 1325 2014-08-15 19:04 ./usr/share/htslib-test/ce#unmap.sam
+-rw-r--r-- root/root 92 2014-08-15 19:04 ./usr/share/htslib-test/test-vcf-sweep.out
+-rw-r--r-- root/root 665 2014-08-15 19:04 ./usr/share/htslib-test/c1#pad3.sam
+
+
+tabix_1.0-1_amd64.deb
+─────────────────────
+
+ new debian package, version 2.0.
+ size 189596 bytes: control archive=931 bytes.
+ 844 bytes, 19 lines control
+ 298 bytes, 5 lines md5sums
+ Package: tabix
+ Source: htslib
+ Version: 1.0-1
+ Architecture: amd64
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 761
+ Depends: libc6 (>= 2.15), zlib1g (>= 1:1.2.0.2)
+ Section: science
+ Priority: optional
+ Homepage: https://github.com/samtools/htslib
+ Description: generic indexer for TAB-delimited genome position files
+ Tabix indexes files where some columns indicate sequence coordinates: name
+ (usually a chromosme), start and stop. The input data file must be position
+ sorted and compressed by bgzip (provided in this package), which has a gzip
+ like interface. After indexing, tabix is able to quickly retrieve data lines by
+ chromosomal coordinates. Fast data retrieval also works over network if an URI
+ is given as a file name.
+ .
+ This version of tabix is built from the HTSlib source.
+
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/man/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/man/man1/
+-rw-r--r-- root/root 2477 2014-08-18 20:50 ./usr/share/man/man1/tabix.1.gz
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/share/doc/tabix/
+-rw-r--r-- root/root 7175 2014-08-16 18:30 ./usr/share/doc/tabix/copyright
+-rw-r--r-- root/root 561 2014-08-18 20:47 ./usr/share/doc/tabix/changelog.Debian.gz
+drwxr-xr-x root/root 0 2014-08-18 20:50 ./usr/bin/
+-rwxr-xr-x root/root 405176 2014-08-18 20:50 ./usr/bin/tabix
+-rwxr-xr-x root/root 326968 2014-08-18 20:50 ./usr/bin/bgzip
+lrwxrwxrwx root/root 0 2014-08-18 20:50 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1611,95 +1570,95 @@ The following packages will be REMOVED:
sbuild-build-depends-htslib-dummy* sbuild-build-depends-lintian-dummy*
t1utils* zlib1g-dev*
0 upgraded, 0 newly installed, 53 to remove and 0 not upgraded.
-After this operation, 36.6 MB disk space will be freed.
-(Reading database ... 13731 files and directories currently installed.)
-Removing sbuild-build-depends-lintian-dummy ...
-Removing lintian ...
-Purging configuration files for lintian ...
-Removing sbuild-build-depends-htslib-dummy ...
-Removing dh-exec ...
-Removing diffstat ...
-Removing hardening-includes ...
-Removing libapt-pkg-perl ...
-Removing libarchive-zip-perl ...
-Removing libparse-debianchangelog-perl ...
-Removing libclass-accessor-perl ...
-Removing libclone-perl ...
-Removing libemail-valid-perl ...
-Removing libnet-dns-perl ...
-Removing libdigest-hmac-perl ...
-Removing libfile-basedir-perl ...
-Removing libipc-run-perl ...
-Removing libio-pty-perl ...
-Removing libio-socket-inet6-perl ...
-Removing libmailtools-perl ...
-Removing libnet-smtp-ssl-perl ...
-Removing libio-socket-ssl-perl ...
-Removing libio-string-perl ...
-Removing liblist-moreutils-perl ...
-Removing libnet-domain-tld-perl ...
-Removing libnet-ip-perl ...
-Removing libnet-ssleay-perl ...
-Removing libsocket6-perl ...
-Removing libssl1.0.0:amd64 ...
-Purging configuration files for libssl1.0.0:amd64 ...
-Removing libsub-name-perl ...
-Removing libtext-levenshtein-perl ...
-Removing liburi-perl ...
-Removing netbase ...
-Purging configuration files for netbase ...
-Removing patchutils ...
-Removing sbuild-build-depends-core-dummy ...
-Removing t1utils ...
-Removing zlib1g-dev:amd64 ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing libasprintf0c2:amd64 ...
-Removing libcroco3:amd64 ...
-Purging configuration files for libcroco3:amd64 ...
-Removing libglib2.0-0:amd64 ...
-Purging configuration files for libglib2.0-0:amd64 ...
-Removing libffi6:amd64 ...
-Purging configuration files for libffi6:amd64 ...
-Removing libmagic1:amd64 ...
-Purging configuration files for libmagic1:amd64 ...
-Removing libpipeline1:amd64 ...
-Purging configuration files for libpipeline1:amd64 ...
-Removing libunistring0:amd64 ...
-Purging configuration files for libunistring0:amd64 ...
-Removing libxml2:amd64 ...
-Purging configuration files for libxml2:amd64 ...
-Processing triggers for libc-bin ...
+After this operation, 39.0 MB disk space will be freed.
+(Reading database ... 13836 files and directories currently installed.)
+Removing sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Removing lintian (2.5.25) ...
+Purging configuration files for lintian (2.5.25) ...
+Removing sbuild-build-depends-htslib-dummy (0.invalid.0) ...
+Removing dh-exec (0.13) ...
+Removing diffstat (1.58-1) ...
+Removing hardening-includes (2.5) ...
+Removing libapt-pkg-perl (0.1.29+b2) ...
+Removing libarchive-zip-perl (1.37-2) ...
+Removing libparse-debianchangelog-perl (1.2.0-1) ...
+Removing libclass-accessor-perl (0.34-1) ...
+Removing libclone-perl (0.37-1+b1) ...
+Removing libemail-valid-perl (1.194-1) ...
+Removing libnet-dns-perl (0.78-1+b1) ...
+Removing libdigest-hmac-perl (1.03+dfsg-1) ...
+Removing libfile-basedir-perl (0.03-1) ...
+Removing libipc-run-perl (0.92-1) ...
+Removing libio-pty-perl (1:1.08-1+b4) ...
+Removing libio-socket-inet6-perl (2.72-1) ...
+Removing libmailtools-perl (2.12-1) ...
+Removing libnet-smtp-ssl-perl (1.01-3) ...
+Removing libio-socket-ssl-perl (1.997-2) ...
+Removing libio-string-perl (1.08-3) ...
+Removing liblist-moreutils-perl (0.33-2+b1) ...
+Removing libnet-domain-tld-perl (1.72-1) ...
+Removing libnet-ip-perl (1.26-1) ...
+Removing libnet-ssleay-perl (1.65-1+b1) ...
+Removing libsocket6-perl (0.25-1+b1) ...
+Removing libssl1.0.0:amd64 (1.0.1i-2) ...
+Purging configuration files for libssl1.0.0:amd64 (1.0.1i-2) ...
+Removing libsub-name-perl (0.07-1+b1) ...
+Removing libtext-levenshtein-perl (0.09-1) ...
+Removing liburi-perl (1.64-1) ...
+Removing netbase (5.2) ...
+Purging configuration files for netbase (5.2) ...
+Removing patchutils (0.3.3-1) ...
+Removing sbuild-build-depends-core-dummy (0.invalid.0) ...
+Removing t1utils (1.37-2) ...
+Removing zlib1g-dev:amd64 (1:1.2.8.dfsg-2) ...
+Removing debhelper (9.20140817) ...
+Removing man-db (2.6.7.1-1) ...
+Purging configuration files for man-db (2.6.7.1-1) ...
+Removing bsdmainutils (9.0.5) ...
+Purging configuration files for bsdmainutils (9.0.5) ...
+Removing file (1:5.19-1) ...
+Removing po-debconf (1.0.16+nmu3) ...
+Removing intltool-debian (0.35.0+20060710.1) ...
+Removing gettext (0.19.2-1) ...
+Removing gettext-base (0.19.2-1) ...
+Removing groff-base (1.22.2-6) ...
+Purging configuration files for groff-base (1.22.2-6) ...
+Removing libasprintf0c2:amd64 (0.19.2-1) ...
+Removing libcroco3:amd64 (0.6.8-3) ...
+Purging configuration files for libcroco3:amd64 (0.6.8-3) ...
+Removing libglib2.0-0:amd64 (2.40.0-4) ...
+Purging configuration files for libglib2.0-0:amd64 (2.40.0-4) ...
+Removing libffi6:amd64 (3.1-2) ...
+Purging configuration files for libffi6:amd64 (3.1-2) ...
+Removing libmagic1:amd64 (1:5.19-1) ...
+Purging configuration files for libmagic1:amd64 (1:5.19-1) ...
+Removing libpipeline1:amd64 (1.3.0-1) ...
+Purging configuration files for libpipeline1:amd64 (1.3.0-1) ...
+Removing libunistring0:amd64 (0.9.3-5.2) ...
+Purging configuration files for libunistring0:amd64 (0.9.3-5.2) ...
+Removing libxml2:amd64 (2.9.1+dfsg1-4) ...
+Purging configuration files for libxml2:amd64 (2.9.1+dfsg1-4) ...
+Processing triggers for libc-bin (2.19-9) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: amd64
-Build-Space: 28664
-Build-Time: 69
+Build-Space: 39704
+Build-Time: 101
Distribution: unstable
Host Architecture: amd64
-Install-Time: 12
-Job: htslib_0.2.0~rc3-1.dsc
+Install-Time: 15
+Job: htslib_1.0-1.dsc
Lintian: pass
Machine Architecture: amd64
Package: htslib
-Package-Time: 86
-Source-Version: 0.2.0~rc3-1
-Space: 28664
+Package-Time: 127
+Source-Version: 1.0-1
+Space: 39704
Status: successful
-Version: 0.2.0~rc3-1
+Version: 1.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20131116-1538
-Build needed 00:01:26, 28664k disc space
+Finished at 20140818-2051
+Build needed 00:02:07, 39704k disc space
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htslib.git
More information about the debian-med-commit
mailing list