htslib →
0.2.0~rc3-1 →
armhf → 2014-06-20 09:15:08
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ htslib 0.2.0~rc3-1 (armhf) 20 Jun 2014 09:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: htslib
Version: 0.2.0~rc3-1
Source Version: 0.2.0~rc3-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/htslib-eJPrJj/htslib-0.2.0~rc3' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/htslib-eJPrJj' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-54dcd873-7517-40bd-b660-63dc2a9fef73' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7328 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8246 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.6 MB in 30s (506 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'htslib' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/htslib.git -b debian/unstable
Need to get 936 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main htslib 0.2.0~rc3-1 (dsc) [2039 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main htslib 0.2.0~rc3-1 (tar) [923 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main htslib 0.2.0~rc3-1 (diff) [10.5 kB]
Fetched 936 kB in 0s (4006 kB/s)
Download complete and in download only mode
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-Scxplm/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
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 2 not upgraded.
Need to get 0 B/812 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 ... 11817 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-KOBEIT/apt_archive/sbuild-build-depends-htslib-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install htslib build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils debhelper dh-exec file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper dh-exec file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
sbuild-build-depends-htslib-dummy zlib1g-dev
0 upgraded, 20 newly installed, 0 to remove and 2 not upgraded.
Need to get 8506 kB/8507 kB of archives.
After this operation, 23.3 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.7.1-1 [964 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-2 [29.2 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.18-1 [229 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-3 [2247 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.18-1 [57.2 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-2 [112 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-2 [1136 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140613 [692 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1+rpi1 [192 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main dh-exec armhf 0.12 [24.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8506 kB in 1s (4325 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11817 files and directories currently installed.)
Preparing to unpack .../libpipeline1_1.3.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.3.0-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.2-5_armhf.deb ...
Unpacking groff-base (1.22.2-5) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.5_armhf.deb ...
Unpacking bsdmainutils (9.0.5) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.6.7.1-1_armhf.deb ...
Unpacking man-db (2.6.7.1-1) ...
Selecting previously unselected package libasprintf0c2:armhf.
Preparing to unpack .../libasprintf0c2_0.18.3.2-2_armhf.deb ...
Unpacking libasprintf0c2:armhf (0.18.3.2-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.18-1_armhf.deb ...
Unpacking libmagic1:armhf (1:5.18-1) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.1+dfsg1-3_armhf.deb ...
Unpacking libxml2:armhf (2.9.1+dfsg1-3) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.1-2_armhf.deb ...
Unpacking libffi6:armhf (3.1-2) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.40.0-3_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.40.0-3) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.8-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.8-2) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.18-1_armhf.deb ...
Unpacking file (1:5.18-1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.18.3.2-2_armhf.deb ...
Unpacking gettext-base (0.18.3.2-2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.18.3.2-2_armhf.deb ...
Unpacking gettext (0.18.3.2-2) ...
Selecting previously unselected package intltool-debian.
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.
Preparing to unpack .../po-debconf_1.0.16+nmu2_all.deb ...
Unpacking po-debconf (1.0.16+nmu2) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20140613_all.deb ...
Unpacking debhelper (9.20140613) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-1+rpi1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-1+rpi1) ...
Selecting previously unselected package dh-exec.
Preparing to unpack .../dh-exec_0.12_armhf.deb ...
Unpacking dh-exec (0.12) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
Preparing to unpack .../sbuild-build-depends-htslib-dummy.deb ...
Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.3.0-1) ...
Setting up groff-base (1.22.2-5) ...
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 (2.6.7.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3.2-2) ...
Setting up libmagic1:armhf (1:5.18-1) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.40.0-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up file (1:5.18-1) ...
Setting up gettext-base (0.18.3.2-2) ...
Setting up gettext (0.18.3.2-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20140613) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1+rpi1) ...
Setting up dh-exec (0.12) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-1) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.14-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140604-3 dpkg-dev_1.17.10 g++-4.9_4.9.0-6 gcc-4.8_4.8.3-3 gcc-4.9_4.9.0-6 libc6-dev_2.19-1 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 linux-libc-dev_3.14.4-1+rpi1
Package versions: apt_1.0.3 base-files_7.3+rpi1 base-passwd_3.5.28 bash_4.3-7 binutils_2.24.51.20140604-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.9.0-3 cpp-4.8_4.8.3-3 cpp-4.9_4.9.0-6 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debianutils_4.4 dh-exec_0.12 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1 e2fsprogs_1.42.10-1 fakeroot_1.18.4-2 file_1:5.18-1 findutils_4.4.2-8 g++_4:4.9.0-3 g++-4.9_4.9.0-6 gcc_4:4.9.0-3 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-3 gcc-4.8-base_4.8.3-3 gcc-4.9_4.9.0-6 gcc-4.9-base_4.9.0-6 gettext_0.18.3.2-2 gettext-base_0.18.3.2-2 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.18-2 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 init-system-helpers_1.18 initramfs-tools_0.115 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.3 libasan0_4.8.3-3 libasan1_4.9.0-6 libasprintf0c2_0.18.3.2-2 libatomic1_4.9.0-6 libattr1_1:2.4.47-1 libaudit-common_1:2.3.6-1 libaudit1_1:2.3.6-1 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-5 libc-bin_2.19-1 libc-dev-bin_2.19-1 libc6_2.19-1 libc6-dev_2.19-1 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.10-1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.4-1 libdpkg-perl_1.17.10 libffi6_3.1-2 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.3-3 libgcc-4.9-dev_4.9.0-6 libgcc1_1:4.9.0-6 libgdbm3_1.8.3-12 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.0-6 libisl10_0.12.2-1 libklibc_2.0.3-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-8 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.18-1 libmount1_2.20.1-5.8 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpcre3_1:8.31-5 libpipeline1_1.3.0-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-5 libreadline6_6.3-6 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-16 libss2_1.42.10-1 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140118-1 libubsan0_4.9.0-6 libudev1_204-8 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.14.4-1+rpi1 login_1:4.2-2 lsb-base_4.1+Debian12+rpi1 make_4.0-8 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.8 multiarch-support_2.19-1 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-4 perl-base_5.18.2-4 perl-modules_5.18.2-4 plymouth_0.8.8-17 po-debconf_1.0.16+nmu2 procps_1:3.3.9-5 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tzdata_2014e-1 udev_204-8 util-linux_2.20.1-5.8 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1+rpi1 zlib1g-dev_1:1.2.8.dfsg-1+rpi1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Nov 16 06:40:38 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./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
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-54dcd873-7517-40bd-b660-63dc2a9fef73
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package htslib
dpkg-buildpackage: source version 0.2.0~rc3-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build htslib-0.2.0~rc3
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 distclean
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 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/*.debhelper.log
rm -f debian/files
find . \( \( -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
rm -f *-stamp
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
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:9:32: 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:9:32: 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:888:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&x, 1, sizeof(x), idx);
^
bgzf.c:899:13: 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:900:13: 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:907:13: 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:908:13: 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:823:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic, 1, 4, fp);
^
hts.c:824:3: 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:223:3: 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:236:4: 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:203:3: 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:423:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, &end, sizeof(int64_t));
^
razf.c:431:3: 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:124:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, &rz->index->size, sizeof(int));
^
razf.c:133:2: 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:139:2: 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:818:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &rz->in, sizeof(int64_t));
^
razf.c:819:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &rz->out, sizeof(int64_t));
^
razf.c:822:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &v64, sizeof(int64_t));
^
razf.c:824:4: 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:260:4: 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:96:12: 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:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, &v32, sizeof(uint32_t));
^
razf.c:106:2: 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:107:2: 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:461:5: 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:464:3: 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:758:3: 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
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:9:32: 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:9:32: 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:888:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&x, 1, sizeof(x), idx);
^
bgzf.c:899:13: 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:900:13: 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:907:13: 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:908:13: 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:823:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic, 1, 4, fp);
^
hts.c:824:3: 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:223:3: 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:236:4: 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:203:3: 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:423:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, &end, sizeof(int64_t));
^
razf.c:431:3: 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:124:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, &rz->index->size, sizeof(int));
^
razf.c:133:2: 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:139:2: 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:818:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &rz->in, sizeof(int64_t));
^
razf.c:819:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &rz->out, sizeof(int64_t));
^
razf.c:822:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &v64, sizeof(int64_t));
^
razf.c:824:4: 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:260:4: 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:96:12: 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:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, &v32, sizeof(uint32_t));
^
razf.c:106:2: 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:107:2: 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:461:5: 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:464:3: 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:758:3: 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.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico -lz
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 -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 -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 -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 -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 -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»'
debian/rules override_dh_auto_test
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test
make -j1 test
make[2]: Entering directory '/«PKGBUILDDIR»'
test/fieldarith test/fieldarith.sam
test/hfile
cd test && ./test_view.pl
=== Testing aux#aux.sam, ref aux.fa ===
./test_view -S -b aux#aux.sam > aux#aux.tmp.bam
./test_view aux#aux.tmp.bam > aux#aux.tmp.bam.sam_
Bus error
FAIL
./compare_sam.pl aux#aux.sam aux#aux.tmp.bam.sam_
EOF on aux#aux.sam
FAIL
./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_
Bus error
FAIL
./compare_sam.pl aux#aux.sam aux#aux.tmp.cram.sam_
EOF on aux#aux.sam
FAIL
./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_
Bus error
FAIL
./compare_sam.pl aux#aux.sam aux#aux.tmp.bam.cram.bam.sam_
EOF on aux#aux.sam
FAIL
=== Testing c1#bounds.sam, ref c1.fa ===
./test_view -S -b c1#bounds.sam > c1#bounds.tmp.bam
./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
./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_
./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_
=== Testing c1#clip.sam, ref c1.fa ===
./test_view -S -b c1#clip.sam > c1#clip.tmp.bam
./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
./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_
./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_
=== Testing c1#pad1.sam, ref c1.fa ===
./test_view -S -b c1#pad1.sam > c1#pad1.tmp.bam
./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
./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_
./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_
=== Testing c1#pad2.sam, ref c1.fa ===
./test_view -S -b c1#pad2.sam > c1#pad2.tmp.bam
./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
./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_
./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_
=== Testing c1#pad3.sam, ref c1.fa ===
./test_view -S -b c1#pad3.sam > c1#pad3.tmp.bam
./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
./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_
./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_
=== Testing ce#1.sam, ref ce.fa ===
./test_view -S -b ce#1.sam > ce#1.tmp.bam
./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_
./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_
./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_
=== Testing ce#2.sam, ref ce.fa ===
./test_view -S -b ce#2.sam > ce#2.tmp.bam
./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_
./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_
./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_
=== Testing ce#5.sam, ref ce.fa ===
./test_view -S -b ce#5.sam > ce#5.tmp.bam
./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_
./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_
./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_
=== Testing ce#5b.sam, ref ce.fa ===
./test_view -S -b ce#5b.sam > ce#5b.tmp.bam
./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
./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_
./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_
=== Testing ce#large_seq.sam, ref ce.fa ===
./test_view -S -b ce#large_seq.sam > ce#large_seq.tmp.bam
./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
./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_
./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_
=== Testing ce#tag_depadded.sam, ref ce.fa ===
./test_view -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
./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_
./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_
=== Testing ce#tag_padded.sam, ref ce.fa ===
./test_view -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
./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_
./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_
=== Testing ce#unmap.sam, ref ce.fa ===
./test_view -S -b ce#unmap.sam > ce#unmap.tmp.bam
./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
./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_
./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_
=== Testing ce#unmap1.sam, ref ce.fa ===
./test_view -S -b ce#unmap1.sam > ce#unmap1.tmp.bam
./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
./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_
./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_
=== Testing ce#unmap2.sam, ref ce.fa ===
./test_view -S -b ce#unmap2.sam > ce#unmap2.tmp.bam
./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
./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_
./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_
=== Testing xx#blank.sam, ref xx.fa ===
./test_view -S -b xx#blank.sam > xx#blank.tmp.bam
./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
./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_
./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_
=== Testing xx#large_aux.sam, ref xx.fa ===
./test_view -S -b xx#large_aux.sam > xx#large_aux.tmp.bam
./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
./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_
./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_
=== Testing xx#large_aux2.sam, ref xx.fa ===
./test_view -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
./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_
./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_
=== Testing xx#minimal.sam, ref xx.fa ===
./test_view -S -b xx#minimal.sam > xx#minimal.tmp.bam
./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
./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_
./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_
=== Testing xx#pair.sam, ref xx.fa ===
./test_view -S -b xx#pair.sam > xx#pair.tmp.bam
./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
./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_
./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_
=== Testing xx#rg.sam, ref xx.fa ===
./test_view -S -b xx#rg.sam > xx#rg.tmp.bam
./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
./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_
./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_
=== Testing xx#triplet.sam, ref xx.fa ===
./test_view -S -b xx#triplet.sam > xx#triplet.tmp.bam
./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
./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_
./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_
=== Testing xx#unsorted.sam, ref xx.fa ===
./test_view -S -b xx#unsorted.sam > xx#unsorted.tmp.bam
./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
./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_
./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_
Successes 234
Failures 6
make[2]: *** [test] Error 1
Makefile:202: recipe for target 'test' failed
make[2]: Leaving directory '/«PKGBUILDDIR»'
dh_auto_test: make -j1 test returned exit code 2
make[1]: *** [override_dh_auto_test] Error 2
debian/rules:9: recipe for target 'override_dh_auto_test' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
debian/rules:6: recipe for target 'build-arch' failed
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140620-0913
Finished
────────
E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 28448
Build-Time: 349
Distribution: jessie-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 129
Job: htslib_0.2.0~rc3-1
Machine Architecture: armhf
Package: htslib
Package-Time: 530
Source-Version: 0.2.0~rc3-1
Space: 28448
Status: attempted
Version: 0.2.0~rc3-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140620-0913
Build needed 00:08:50, 28448k disc space