Raspbian Package Auto-Building

Build log for htslib (0.2.0~rc3-1) on armhf

htslib0.2.0~rc3-1armhf → 2013-12-12 15:22:07

sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-04

╔══════════════════════════════════════════════════════════════════════════════╗
║ htslib 0.2.0~rc3-1 (armhf)                                 12 Dec 2013 15:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝

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-vv4RVQ/htslib-0.2.0~rc3' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/htslib-vv4RVQ' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-a23b5a96-d950-4529-aea9-a293e2a14805' 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 [7093 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8218 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.3 MB in 30s (499 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 (1481 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-hQiUq0/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 31 not upgraded.
Need to get 0 B/704 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 ... 11477 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
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-rHDgbs/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 31 not upgraded.
Need to get 8586 kB/8586 kB of archives.
After this operation, 22.6 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.4-1 [36.9 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 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 2.6.5-2 [949 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.1-2 [29.5 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 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 3.0.13-4 [19.8 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.4-1 [1907 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 1:5.14-2 [53.8 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.1-2 [135 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.1-2 [1829 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 9.20131127 [687 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 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 8586 kB in 1s (4360 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11477 files and directories currently installed.)
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.4-1_armhf.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.22.2-3_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_armhf.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.5-2_armhf.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.3.1-2_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
Unpacking libmagic1:armhf (from .../libmagic1_1%3a5.14-2_armhf.deb) ...
Selecting previously unselected package libxml2:armhf.
Unpacking libxml2:armhf (from .../libxml2_2.9.1+dfsg1-3_armhf.deb) ...
Selecting previously unselected package libffi6:armhf.
Unpacking libffi6:armhf (from .../libffi6_3.0.13-4_armhf.deb) ...
Selecting previously unselected package libglib2.0-0:armhf.
Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.36.4-1_armhf.deb) ...
Selecting previously unselected package libcroco3:armhf.
Unpacking libcroco3:armhf (from .../libcroco3_0.6.8-2_armhf.deb) ...
Selecting previously unselected package libunistring0:armhf.
Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_1%3a5.14-2_armhf.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.3.1-2_armhf.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.3.1-2_armhf.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
Unpacking debhelper (from .../debhelper_9.20131127_all.deb) ...
Selecting previously unselected package zlib1g-dev:armhf.
Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.8.dfsg-1_armhf.deb) ...
Selecting previously unselected package dh-exec.
Unpacking dh-exec (from .../dh-exec_0.12_armhf.deb) ...
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:armhf (1.2.4-1) ...
Setting up groff-base (1.22.2-3) ...
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) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3.1-2) ...
Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libffi6:armhf (3.0.13-4) ...
Setting up libglib2.0-0:armhf (2.36.4-1) ...
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 (1:5.14-2) ...
Setting up gettext-base (0.18.3.1-2) ...
Setting up gettext (0.18.3.1-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20131127) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up dh-exec (0.12) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin ...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 3.11.0-armv7-x13 armhf (armv7l)
Toolchain package versions: binutils_2.23.90.20131017-1 dpkg-dev_1.16.12 g++-4.8_4.8.2-1+rpi1 gcc-4.8_4.8.2-1+rpi1 libc6-dev_2.17-93 libstdc++-4.8-dev_4.8.2-1+rpi1 libstdc++6_4.8.2-1+rpi1 linux-libc-dev_3.10.1-1+rpi1+b2
Package versions: apt_0.9.12.1+rpi1 base-files_7.2+rpi1 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 cpio_2.11+dfsg-1 cpp_4:4.8.1-3 cpp-4.8_4.8.2-1+rpi1 dash_0.5.7-3 debconf_1.5.51 debconf-i18n_1.5.51 debfoster_2.7-1.2 debhelper_9.20131127 debianutils_4.4 dh-exec_0.12 diffutils_1:3.3-1 dpkg_1.16.12 dpkg-dev_1.16.12 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-6 g++_4:4.8.1-3 g++-4.8_4.8.2-1+rpi1 gcc_4:4.8.1-3 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-4+rpi1 gcc-4.7-base_4.7.3-4+rpi1 gcc-4.8_4.8.2-1+rpi1 gcc-4.8-base_4.8.2-1+rpi1 gettext_0.18.3.1-2 gettext-base_0.18.3.1-2 gnupg_1.4.15-1.1 gpgv_1.4.15-1.1 grep_2.14-4 groff-base_1.22.2-3 gzip_1.6-2 hostname_3.14 initramfs-tools_0.114 initscripts_2.88dsf-43 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.52-1 libapt-pkg4.12_0.9.12.1+rpi1 libasan0_4.8.2-1+rpi1 libasprintf0c2_0.18.3.1-2 libatomic1_4.8.2-1+rpi1 libattr1_1:2.4.47-1 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-5 libc-bin_2.17-93 libc-dev-bin_2.17-93 libc6_2.17-93 libc6-dev_2.17-93 libcap2_1:2.22-1.2 libcloog-isl4_0.18.1-1 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdbus-1-3_1.6.18-1 libdpkg-perl_1.16.12 libffi6_3.0.13-4 libgc1c2_1:7.2d-5 libgcc-4.8-dev_4.8.2-1+rpi1 libgcc1_1:4.8.2-1+rpi1 libgdbm3_1.8.3-12 libglib2.0-0_2.36.4-1 libgmp10_2:5.1.2+dfsg-3 libgomp1_4.8.2-1+rpi1 libisl10_0.12.1-1 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.5 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libnih-dbus1_1.0.3-4.1+b1 libnih1_1.0.3-4.1+b1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libprocps0_1:3.3.4-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-3+rpi1 libsemanage-common_2.1.10-3+rpi1 libsemanage1_2.1.10-3+rpi1 libsepol1_2.1.9-2 libslang2_2.2.4-15 libss2_1.42.8-1 libstdc++-4.8-dev_4.8.2-1+rpi1 libstdc++6_4.8.2-1+rpi1 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9+20130608-1 libudev1_204-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.10.1-1+rpi1+b2 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.5 mountall_2.52 multiarch-support_2.17-93 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-3 perl_5.18.1-4 perl-base_5.18.1-4 perl-modules_5.18.1-4 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.2.2-2 sensible-utils_0.0.9 sysv-rc_2.88dsf-43 sysvinit_2.88dsf-43 sysvinit-utils_2.88dsf-43 tar_1.26+dfsg-8 tzdata_2013d-1 udev_204-5 util-linux_2.20.1-5.5 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1

┌──────────────────────────────────────────────────────────────────────────────┐
│ 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
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=POSIX
LOGNAME=root
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
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-a23b5a96-d950-4529-aea9-a293e2a14805
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=172.17.0.6 43532 22
SSH_CONNECTION=172.17.0.6 43532 172.17.2.4 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=root
_=/etc/init.d/buildd

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package htslib
dpkg-buildpackage: source version 0.2.0~rc3-1
 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" "CPPFLAGS=-I. -DSAMTOOLS=1 " LDFLAGS=
make[2]: Entering directory `/«PKGBUILDDIR»'
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o kfunc.o kfunc.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o knetfile.o knetfile.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o kstring.o kstring.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o bgzf.o bgzf.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o faidx.o faidx.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o hfile.o hfile.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "0.0.1"' > version.h
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o hts.o hts.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o razf.o razf.c
gcc -g -O2 -I. -DSAMTOOLS=1  -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 -I. -DSAMTOOLS=1  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o tbx.o tbx.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o vcf.o vcf.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o vcfutils.o vcfutils.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/files.o cram/files.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/md5.o cram/md5.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o cram/vlen.o cram/vlen.c
gcc -g -O2 -I. -DSAMTOOLS=1  -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 -I. -DSAMTOOLS=1  -fpic -c -o kfunc.pico kfunc.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o knetfile.pico knetfile.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o kstring.pico kstring.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o bgzf.pico bgzf.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o faidx.pico faidx.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o hfile.pico hfile.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o hts.pico hts.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o razf.pico razf.c
gcc -g -O2 -I. -DSAMTOOLS=1  -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 -I. -DSAMTOOLS=1  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o tbx.pico tbx.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o vcf.pico vcf.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/files.pico cram/files.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/md5.pico cram/md5.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/thread_pool.pico cram/thread_pool.c
gcc -g -O2 -I. -DSAMTOOLS=1  -fpic -c -o cram/vlen.pico cram/vlen.c
gcc -g -O2 -I. -DSAMTOOLS=1  -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 -I. -DSAMTOOLS=1  -c -o test/fieldarith.o test/fieldarith.c
gcc -pthread  -o test/fieldarith test/fieldarith.o libhts.a  -lz
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o test/hfile.o test/hfile.c
gcc  -o test/hfile test/hfile.o libhts.a  -lz
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o test/test_view.o test/test_view.c
gcc -pthread  -o test/test_view test/test_view.o libhts.a  -lz
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -pthread  -o test/test-vcf-api test/test-vcf-api.o libhts.a  -lz
gcc -g -O2 -I. -DSAMTOOLS=1  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -pthread  -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
make[2]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test: make -j1 test returned exit code 2
make[1]: *** [override_dh_auto_test] Error 2
make[1]: Leaving directory `/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
Build finished at 20131212-1523

Finished
────────

E: Build failure (dpkg-buildpackage died)

┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Build Architecture: armhf
Build-Space: 27520
Build-Time: 312
Distribution: jessie-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 169
Job: htslib_0.2.0~rc3-1
Machine Architecture: armhf
Package: htslib
Package-Time: 533
Source-Version: 0.2.0~rc3-1
Space: 27520
Status: attempted
Version: 0.2.0~rc3-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20131212-1523
Build needed 00:08:53, 27520k disc space