vcftools →
0.1.13+dfsg-1 →
armhf → 2015-09-10 03:58:05
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ vcftools 0.1.13+dfsg-1 (armhf) 10 Sep 2015 03:44 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: vcftools
Version: 0.1.13+dfsg-1
Source Version: 0.1.13+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/vcftools-lszyAH/vcftools-0.1.13+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/vcftools-lszyAH' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-d2bf5400-8075-41b6-997b-d747b0512165' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8312 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.2 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
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Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'vcftools' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/vcftools/trunk
Need to get 625 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main vcftools 0.1.13+dfsg-1 (dsc) [2035 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main vcftools 0.1.13+dfsg-1 (tar) [606 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main vcftools 0.1.13+dfsg-1 (diff) [16.6 kB]
Fetched 625 kB in 0s (3392 kB/s)
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Check architectures
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-djzgom/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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Get:1 file: ./ Release.gpg [299 B]
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Ign file: ./ Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ 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 13 not upgraded.
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-vcftools-dummy' in '/«BUILDDIR»/resolver-77pKPN/apt_archive/sbuild-build-depends-vcftools-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install vcftools 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 file gettext gettext-base groff-base intltool-debian
libasprintf0v5 libcroco3 libffi6 libglib2.0-0 libmagic1 libpipeline1
libunistring0 libxml2 man-db po-debconf zlib1g 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 xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian
libasprintf0v5 libcroco3 libffi6 libglib2.0-0 libmagic1 libpipeline1
libunistring0 libxml2 man-db po-debconf sbuild-build-depends-vcftools-dummy
zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 19 newly installed, 0 to remove and 12 not upgraded.
Need to get 8876 kB/8877 kB of archives.
After this operation, 26.0 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main zlib1g armhf 1:1.2.8.dfsg-2+b1 [80.9 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.2-1 [973 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libasprintf0v5 armhf 0.19.5.1-1 [32.0 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.5.1-1 [118 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.5.1-1 [1386 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150811 [817 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking sbuild-build-depends-vcftools-dummy (0.invalid.0) ...
Setting up groff-base (1.22.3-1) ...
Setting up bsdmainutils (9.0.6) ...
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 libpipeline1:armhf (1.4.1-1) ...
Setting up man-db (2.7.2-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
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Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150811) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up sbuild-build-depends-vcftools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-19) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-4.9_4.9.3-4 g++-5_5.2.1-16+rpi1 gcc-4.9_4.9.3-4 gcc-5_5.2.1-16+rpi1 libc6-dev_2.19-19 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.10 base-files_9.2+rpi1 base-passwd_3.5.38 bash_4.3-13 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.26.2-9 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi1 cpp-4.9_4.9.3-4 cpp-5_5.2.1-16+rpi1 dash_0.5.7-4 debconf_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:5.2.1-4+rpi1 g++-4.9_4.9.3-4 g++-5_5.2.1-16+rpi1 gcc_4:5.2.1-4+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-4 gcc-4.9_4.9.3-4 gcc-4.9-base_4.9.3-4 gcc-5_5.2.1-16+rpi1 gcc-5-base_5.2.1-16+rpi1 gettext_0.19.5.1-1 gettext-base_0.19.5.1-1 gnupg_1.4.19-5 gpgv_1.4.19-5 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.23 init-system-helpers_1.23 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.9.2-3 libapt-pkg4.12_1.0.9.10 libasan1_4.9.3-4 libasan2_5.2.1-16+rpi1 libasprintf0v5_0.19.5.1-1 libatomic1_5.2.1-16+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-1 libaudit1_1:2.4.4-1 libblkid1_2.26.2-9 libbz2-1.0_1.0.6-8 libc-bin_2.19-19 libc-dev-bin_2.19-19 libc6_2.19-19 libc6-dev_2.19-19 libcap2_1:2.24-11 libcap2-bin_1:2.24-11 libcc1-0_5.2.1-16+rpi1 libcloog-isl4_0.18.3-1 libcomerr2_1.42.13-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.20-1 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.104-1 libdpkg-perl_1.18.2 libdrm2_2.4.64-1 libfakeroot_1.20.2-1 libfdisk1_2.26.2-9 libffi6_3.2.1-3 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.3-4 libgcc-5-dev_5.2.1-16+rpi1 libgcc1_1:5.2.1-16+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-7+rpi1 libgomp1_5.2.1-16+rpi1 libgpg-error0_1.19-2 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.05-9 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.22+15-2 libmount1_2.26.2-9 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20150810-1 libncursesw5_6.0+20150810-1 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-7 libpipeline1_1.4.1-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libreadline6_6.3-8 libseccomp2_2.2.3-1 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.26.2-9 libss2_1.42.13-1 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 libsystemd0_225-1 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20150810-1 libubsan0_5.2.1-16+rpi1 libudev1_225-1 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-5 libuuid1_2.26.2-9 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.2-1 mawk_1.3.3-17 mount_2.26.2-9 mountall_2.54 multiarch-support_2.19-19 ncurses-base_6.0+20150810-1 ncurses-bin_6.0+20150810-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.10-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-vcftools-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_225-1 systemd-sysv_225-1 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-1 tzdata_2015f-1 udev_225-1 util-linux_2.26.2-9 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
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gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Aug 9 07:52:02 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./vcftools_0.1.13+dfsg-1.dsc
dpkg-source: info: extracting vcftools in vcftools-0.1.13+dfsg
dpkg-source: info: unpacking vcftools_0.1.13+dfsg.orig.tar.gz
dpkg-source: info: unpacking vcftools_0.1.13+dfsg-1.debian.tar.xz
dpkg-source: info: applying make.patch
dpkg-source: info: applying use-dpkg-buildflags.patch
Check disc space
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Sufficient free space for build
User Environment
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DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-d2bf5400-8075-41b6-997b-d747b0512165
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package vcftools
dpkg-buildpackage: source version 0.1.13+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build vcftools-0.1.13+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
make[2]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/cpp'
make[2]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/cpp'
make[2]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/perl'
make[2]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/perl'
make[1]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
debian/rules override_dh_clean
make[1]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
dh_clean
rm -f debian/vcftools.substvars
rm -f debian/vcftools.*.debhelper
rm -rf debian/vcftools/
rm -rf debian/.debhelper/
rm -f debian/*.debhelper.log
rm -f debian/files
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -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
# [ -r Makefile ] && make clean ?
make[1]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
dh_auto_build -a
make -j1
make[1]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
mkdir -p /«BUILDDIR»/vcftools-0.1.13+dfsg//bin; mkdir -p /«BUILDDIR»/vcftools-0.1.13+dfsg//lib/perl5/site_perl; \
for dir in cpp perl; do cd ${dir} && make && cd ..; done
make[2]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/cpp'
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro vcftools.cpp -o vcftools.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro vcftools.cpp > vcftools.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro bcf_file.cpp -o bcf_file.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro bcf_file.cpp > bcf_file.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro vcf_file.cpp -o vcf_file.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro vcf_file.cpp > vcf_file.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file.cpp -o variant_file.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file.cpp > variant_file.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro header.cpp -o header.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro header.cpp > header.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro bcf_entry.cpp -o bcf_entry.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro bcf_entry.cpp > bcf_entry.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro vcf_entry.cpp -o vcf_entry.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro vcf_entry.cpp > vcf_entry.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro entry.cpp -o entry.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro entry.cpp > entry.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro entry_getters.cpp -o entry_getters.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro entry_getters.cpp > entry_getters.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro entry_setters.cpp -o entry_setters.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro entry_setters.cpp > entry_setters.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro vcf_entry_setters.cpp -o vcf_entry_setters.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro vcf_entry_setters.cpp > vcf_entry_setters.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro bcf_entry_setters.cpp -o bcf_entry_setters.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro bcf_entry_setters.cpp > bcf_entry_setters.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro entry_filters.cpp -o entry_filters.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro entry_filters.cpp > entry_filters.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file_filters.cpp -o variant_file_filters.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file_filters.cpp > variant_file_filters.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file_output.cpp -o variant_file_output.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file_output.cpp > variant_file_output.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro parameters.cpp -o parameters.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro parameters.cpp > parameters.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file_format_convert.cpp -o variant_file_format_convert.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file_format_convert.cpp > variant_file_format_convert.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file_diff.cpp -o variant_file_diff.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro variant_file_diff.cpp > variant_file_diff.d
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro output_log.cpp -o output_log.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro output_log.cpp > output_log.d
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
bgzf.c: In function 'bgzf_check_EOF':
bgzf.c:60:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
#define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp))
^
bgzf.c:622:2: note: in expansion of macro '_bgzf_read'
_bgzf_read(fp->fp, buf, 28);
^
g++ -c -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro gamma.cpp -o gamma.o
g++ -MM -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-z,relro gamma.cpp > gamma.d
g++ -D_FORTIFY_SOURCE=2 -O2 -D_FILE_OFFSET_BITS=64 vcftools.o bcf_file.o vcf_file.o variant_file.o header.o bcf_entry.o vcf_entry.o entry.o entry_getters.o entry_setters.o vcf_entry_setters.o bcf_entry_setters.o entry_filters.o variant_file_filters.o variant_file_output.o parameters.o variant_file_format_convert.o variant_file_diff.o output_log.o bgzf.o gamma.o -Wl,-z,relro -o vcftools -lz
variant_file_output.o: In function `variant_file::output_interchromosomal_genotype_r2(parameters const&)':
/«BUILDDIR»/vcftools-0.1.13+dfsg/cpp/variant_file_output.cpp:1952: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
cp /«BUILDDIR»/vcftools-0.1.13+dfsg/cpp/vcftools /«BUILDDIR»/vcftools-0.1.13+dfsg//bin/vcftools
make[2]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/cpp'
make[2]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/perl'
make[2]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/perl'
make[1]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f debian/vcftools.substvars
rm -f debian/vcftools.*.debhelper
rm -rf debian/vcftools/
dh_auto_install -a
install -d debian/vcftools
make -j1 install DESTDIR=/«BUILDDIR»/vcftools-0.1.13\+dfsg/debian/vcftools AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
mkdir -p /«BUILDDIR»/vcftools-0.1.13+dfsg//bin; mkdir -p /«BUILDDIR»/vcftools-0.1.13+dfsg//lib/perl5/site_perl; \
for dir in cpp perl; do cd ${dir} && make && cd ..; done
make[2]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/cpp'
make[2]: 'vcftools' is up to date.
make[2]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/cpp'
make[2]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/perl'
make[2]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg/perl'
make[1]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
dh_install -a
install -d debian/vcftools/usr
cp --reflink=auto -a ./bin debian/vcftools/usr/
install -d debian/vcftools/usr/share/perl5
cp --reflink=auto -a ./lib/perl5/site_perl/FaSlice.pm debian/vcftools/usr/share/perl5/
cp --reflink=auto -a ./lib/perl5/site_perl/Vcf.pm debian/vcftools/usr/share/perl5/
cp --reflink=auto -a ./lib/perl5/site_perl/VcfStats.pm debian/vcftools/usr/share/perl5/
dh_installdocs -a
install -d debian/vcftools/usr/share/doc/vcftools
install -p -m0644 debian/copyright debian/vcftools/usr/share/doc/vcftools/copyright
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
dh_installchangelogs perl/ChangeLog
install -p -m0644 debian/changelog debian/vcftools/usr/share/doc/vcftools/changelog.Debian
install -p -m0644 perl/ChangeLog debian/vcftools/usr/share/doc/vcftools/changelog
make[1]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
dh_installexamples -a
install -d debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/annotate-test.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/annotate.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/annotate.txt debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/annotate2.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/annotate3.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/cmp-test-a-3.3.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/cmp-test-a.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/cmp-test-b-3.3.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/cmp-test-b.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/cmp-test.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/concat-a.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/concat-b.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/concat-c.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/concat.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/consensus.fa debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/consensus.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/consensus.out2 debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/consensus.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/contrast.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/contrast.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/fill-an-ac.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/filters.txt debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/fix-ploidy.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/fix-ploidy.samples debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/fix-ploidy.txt debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/fix-ploidy.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/floats.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/indel-stats.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/indel-stats.tab debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/indel-stats.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/invalid-4.0.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/isec-n2-test.vcf.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/merge-test-a.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/merge-test-b.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/merge-test-c.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/merge-test.vcf.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/parse-test.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/perl-api-1.pl debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/query-test.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/shuffle-test.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/subset.indels.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/subset.SNPs.out debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/subset.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/valid-3.3.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/valid-4.0.vcf debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/valid-4.0.vcf.stats debian/vcftools/usr/share/doc/vcftools/examples
cp --reflink=auto -a examples/valid-4.1.vcf debian/vcftools/usr/share/doc/vcftools/examples
dh_installman -a
install -d debian/vcftools/usr/share/man/man1/
install -p -m0644 debian/vcftools.1 debian/vcftools/usr/share/man/man1/vcftools.1
install -p -m0644 debian/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1
install -p -m0644 debian/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-compare.1
install -p -m0644 debian/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-concat.1
install -p -m0644 debian/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-convert.1
install -p -m0644 debian/vcf-isec.1 debian/vcftools/usr/share/man/man1/vcf-isec.1
install -p -m0644 debian/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-merge.1
install -p -m0644 debian/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-query.1
install -p -m0644 debian/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-sort.1
install -p -m0644 debian/vcf-stats.1 debian/vcftools/usr/share/man/man1/vcf-stats.1
install -p -m0644 debian/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-subset.1
install -p -m0644 debian/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1
install -p -m0644 debian/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcf-validator.1
install -p -m0644 debian/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-aa.1
install -p -m0644 debian/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1
install -p -m0644 debian/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1
install -p -m0644 debian/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-fs.1
install -p -m0644 debian/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1
install -p -m0644 debian/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1
install -p -m0644 debian/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1
install -p -m0644 debian/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1
install -p -m0644 debian/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1
install -p -m0644 debian/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1
install -p -m0644 debian/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1
install -p -m0644 debian/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1
man --recode UTF-8 ./vcftools\.1 > vcftools\.1\.new
chmod 644 vcftools.1.new
mv -f vcftools.1.new vcftools.1
man --recode UTF-8 ./vcf\-annotate\.1 > vcf\-annotate\.1\.new
chmod 644 vcf-annotate.1.new
mv -f vcf-annotate.1.new vcf-annotate.1
man --recode UTF-8 ./vcf\-compare\.1 > vcf\-compare\.1\.new
chmod 644 vcf-compare.1.new
mv -f vcf-compare.1.new vcf-compare.1
man --recode UTF-8 ./vcf\-concat\.1 > vcf\-concat\.1\.new
chmod 644 vcf-concat.1.new
mv -f vcf-concat.1.new vcf-concat.1
man --recode UTF-8 ./vcf\-convert\.1 > vcf\-convert\.1\.new
chmod 644 vcf-convert.1.new
mv -f vcf-convert.1.new vcf-convert.1
man --recode UTF-8 ./vcf\-isec\.1 > vcf\-isec\.1\.new
chmod 644 vcf-isec.1.new
mv -f vcf-isec.1.new vcf-isec.1
man --recode UTF-8 ./vcf\-merge\.1 > vcf\-merge\.1\.new
chmod 644 vcf-merge.1.new
mv -f vcf-merge.1.new vcf-merge.1
man --recode UTF-8 ./vcf\-query\.1 > vcf\-query\.1\.new
chmod 644 vcf-query.1.new
mv -f vcf-query.1.new vcf-query.1
man --recode UTF-8 ./vcf\-sort\.1 > vcf\-sort\.1\.new
chmod 644 vcf-sort.1.new
mv -f vcf-sort.1.new vcf-sort.1
man --recode UTF-8 ./vcf\-stats\.1 > vcf\-stats\.1\.new
chmod 644 vcf-stats.1.new
mv -f vcf-stats.1.new vcf-stats.1
man --recode UTF-8 ./vcf\-subset\.1 > vcf\-subset\.1\.new
chmod 644 vcf-subset.1.new
mv -f vcf-subset.1.new vcf-subset.1
man --recode UTF-8 ./vcf\-to\-tab\.1 > vcf\-to\-tab\.1\.new
chmod 644 vcf-to-tab.1.new
mv -f vcf-to-tab.1.new vcf-to-tab.1
man --recode UTF-8 ./vcf\-validator\.1 > vcf\-validator\.1\.new
chmod 644 vcf-validator.1.new
mv -f vcf-validator.1.new vcf-validator.1
man --recode UTF-8 ./fill\-aa\.1 > fill\-aa\.1\.new
chmod 644 fill-aa.1.new
mv -f fill-aa.1.new fill-aa.1
man --recode UTF-8 ./fill\-an\-ac\.1 > fill\-an\-ac\.1\.new
chmod 644 fill-an-ac.1.new
mv -f fill-an-ac.1.new fill-an-ac.1
man --recode UTF-8 ./fill\-rsIDs\.1 > fill\-rsIDs\.1\.new
chmod 644 fill-rsIDs.1.new
mv -f fill-rsIDs.1.new fill-rsIDs.1
man --recode UTF-8 ./fill\-fs\.1 > fill\-fs\.1\.new
chmod 644 fill-fs.1.new
mv -f fill-fs.1.new fill-fs.1
man --recode UTF-8 ./fill\-ref\-md5\.1 > fill\-ref\-md5\.1\.new
chmod 644 fill-ref-md5.1.new
mv -f fill-ref-md5.1.new fill-ref-md5.1
man --recode UTF-8 ./vcf\-consensus\.1 > vcf\-consensus\.1\.new
chmod 644 vcf-consensus.1.new
mv -f vcf-consensus.1.new vcf-consensus.1
man --recode UTF-8 ./vcf\-contrast\.1 > vcf\-contrast\.1\.new
chmod 644 vcf-contrast.1.new
mv -f vcf-contrast.1.new vcf-contrast.1
man --recode UTF-8 ./vcf\-fix\-ploidy\.1 > vcf\-fix\-ploidy\.1\.new
chmod 644 vcf-fix-ploidy.1.new
mv -f vcf-fix-ploidy.1.new vcf-fix-ploidy.1
man --recode UTF-8 ./vcf\-indel\-stats\.1 > vcf\-indel\-stats\.1\.new
chmod 644 vcf-indel-stats.1.new
mv -f vcf-indel-stats.1.new vcf-indel-stats.1
man --recode UTF-8 ./vcf\-phased\-join\.1 > vcf\-phased\-join\.1\.new
chmod 644 vcf-phased-join.1.new
mv -f vcf-phased-join.1.new vcf-phased-join.1
man --recode UTF-8 ./vcf\-shuffle\-cols\.1 > vcf\-shuffle\-cols\.1\.new
chmod 644 vcf-shuffle-cols.1.new
mv -f vcf-shuffle-cols.1.new vcf-shuffle-cols.1
man --recode UTF-8 ./vcf\-tstv\.1 > vcf\-tstv\.1\.new
chmod 644 vcf-tstv.1.new
mv -f vcf-tstv.1.new vcf-tstv.1
dh_lintian -a
install -d debian/vcftools/usr/share/lintian/overrides
install -p -m0644 debian/vcftools.lintian-overrides debian/vcftools/usr/share/lintian/overrides/vcftools
dh_perl -a
(grep -s -v perl:Depends debian/vcftools.substvars; echo perl:Depends=perl) > debian/vcftools.substvars.new
mv debian/vcftools.substvars.new debian/vcftools.substvars
rmdir --ignore-fail-on-non-empty --parents debian/vcftools/usr/share/perl5
dh_link -a
dh_compress -a
cd debian/vcftools
chmod a-x usr/share/man/man1/vcftools.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-tstv.1 usr/share/doc/vcftools/changelog.Debian usr/share/doc/vcftools/changelog usr/share/doc/vcftools/examples/contrast.out usr/share/doc/vcftools/examples/contrast.vcf usr/share/doc/vcftools/examples/filters.txt usr/share/doc/vcftools/examples/fix-ploidy.vcf usr/share/doc/vcftools/examples/valid-4.0.vcf.stats
gzip -9nf usr/share/man/man1/vcftools.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-tstv.1 usr/share/doc/vcftools/changelog.Debian usr/share/doc/vcftools/changelog usr/share/doc/vcftools/examples/contrast.out usr/share/doc/vcftools/examples/contrast.vcf usr/share/doc/vcftools/examples/filters.txt usr/share/doc/vcftools/examples/fix-ploidy.vcf usr/share/doc/vcftools/examples/valid-4.0.vcf.stats
cd '/«BUILDDIR»/vcftools-0.1.13+dfsg'
debian/rules override_dh_fixperms
make[1]: Entering directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
dh_fixperms
find debian/vcftools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/vcftools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/vcftools/usr/share/doc -type f ! -regex 'debian/vcftools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
find debian/vcftools/usr/share/man debian/vcftools/usr/man/ debian/vcftools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools/usr/lib/arm-linux-gnueabihf/perl5/5.20 debian/vcftools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/vcftools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
find debian/vcftools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/vcftools/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
chmod -x debian/vcftools/usr/share/doc/vcftools/examples/*
make[1]: Leaving directory '/«BUILDDIR»/vcftools-0.1.13+dfsg'
dh_strip -a
strip --remove-section=.comment --remove-section=.note debian/vcftools/usr/bin/vcftools
dh_makeshlibs -a
rm -f debian/vcftools/DEBIAN/shlibs
dh_shlibdeps -a
install -d debian/vcftools/DEBIAN
dpkg-shlibdeps -Tdebian/vcftools.substvars debian/vcftools/usr/bin/vcftools
dpkg-shlibdeps: warning: debian/vcftools/usr/bin/vcftools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
echo misc:Depends= >> debian/vcftools.substvars
echo misc:Pre-Depends= >> debian/vcftools.substvars
dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -Pdebian/vcftools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 0644 debian/vcftools/DEBIAN/control
chown 0:0 debian/vcftools/DEBIAN/control
dh_md5sums -a
(cd debian/vcftools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 0644 debian/vcftools/DEBIAN/md5sums
chown 0:0 debian/vcftools/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --build debian/vcftools ..
dpkg-deb: building package 'vcftools' in '../vcftools_0.1.13+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../vcftools_0.1.13+dfsg-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build vcftools-0.1.13+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150910-0358
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
vcftools_0.1.13+dfsg-1_armhf.changes:
─────────────────────────────────────
Format: 1.8
Date: Sun, 09 Aug 2015 08:15:47 +0200
Source: vcftools
Binary: vcftools
Architecture: armhf
Version: 0.1.13+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
vcftools - Collection of tools to work with VCF files
Changes:
vcftools (0.1.13+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Adapt to new uscan
* cme fix dpkg-control
* Priority: optional
* Fix permission of example files
* DEP5 fix
Checksums-Sha1:
21d80835c85b99db45aada625211e4b7009d2908 367180 vcftools_0.1.13+dfsg-1_armhf.deb
Checksums-Sha256:
1c37b9d8534a9ac8fcef791e393812a7a31770bdaac1c5ef57d47905488a57ad 367180 vcftools_0.1.13+dfsg-1_armhf.deb
Files:
def2f2175e5a033e37586dff183a7cf8 367180 science optional vcftools_0.1.13+dfsg-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
vcftools_0.1.13+dfsg-1_armhf.deb
────────────────────────────────
new debian package, version 2.0.
size 367180 bytes: control archive=3476 bytes.
694 bytes, 15 lines control
7323 bytes, 103 lines md5sums
Package: vcftools
Version: 0.1.13+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1247
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.6), perl
Recommends: tabix
Section: science
Priority: optional
Homepage: http://vcftools.sourceforge.net
Description: Collection of tools to work with VCF files
VCFtools is a program package designed for working with VCF files, such as
those generated by the 1000 Genomes Project. The aim of VCFtools is to
provide methods for working with VCF files: validating, merging, comparing
and calculate some basic population genetic statistics.
drwxr-xr-x root/root 0 2015-09-10 03:57 ./
drwxr-xr-x root/root 0 2015-09-10 03:57 ./usr/
drwxr-xr-x root/root 0 2015-09-10 03:57 ./usr/bin/
-rwxr-xr-x root/root 6104 2015-09-10 03:57 ./usr/bin/fill-aa
-rwxr-xr-x root/root 1261 2015-09-10 03:57 ./usr/bin/fill-an-ac
-rwxr-xr-x root/root 8068 2015-09-10 03:57 ./usr/bin/fill-fs
-rwxr-xr-x root/root 6567 2015-09-10 03:57 ./usr/bin/fill-ref-md5
-rwxr-xr-x root/root 51253 2015-09-10 03:57 ./usr/bin/vcf-annotate
-rwxr-xr-x root/root 57390 2015-09-10 03:57 ./usr/bin/vcf-compare
-rwxr-xr-x root/root 10952 2015-09-10 03:57 ./usr/bin/vcf-concat
-rwxr-xr-x root/root 9226 2015-09-10 03:57 ./usr/bin/vcf-consensus
-rwxr-xr-x root/root 8797 2015-09-10 03:57 ./usr/bin/vcf-contrast
-rwxr-xr-x root/root 6176 2015-09-10 03:57 ./usr/bin/vcf-convert
-rwxr-xr-x root/root 10549 2015-09-10 03:57 ./usr/bin/vcf-fix-ploidy
-rwxr-xr-x root/root 4376 2015-09-10 03:57 ./usr/bin/vcf-indel-stats
-rwxr-xr-x root/root 21173 2015-09-10 03:57 ./usr/bin/vcf-isec
-rwxr-xr-x root/root 22988 2015-09-10 03:57 ./usr/bin/vcf-merge
-rwxr-xr-x root/root 23234 2015-09-10 03:57 ./usr/bin/vcf-phased-join
-rwxr-xr-x root/root 15832 2015-09-10 03:57 ./usr/bin/vcf-query
-rwxr-xr-x root/root 2301 2015-09-10 03:57 ./usr/bin/vcf-shuffle-cols
-rwxr-xr-x root/root 3310 2015-09-10 03:57 ./usr/bin/vcf-sort
-rwxr-xr-x root/root 4874 2015-09-10 03:57 ./usr/bin/vcf-stats
-rwxr-xr-x root/root 7706 2015-09-10 03:57 ./usr/bin/vcf-subset
-rwxr-xr-x root/root 2543 2015-09-10 03:57 ./usr/bin/vcf-to-tab
-rwxr-xr-x root/root 1820 2015-09-10 03:57 ./usr/bin/vcf-tstv
-rwxr-xr-x root/root 3353 2015-09-10 03:57 ./usr/bin/vcf-validator
-rwxr-xr-x root/root 698416 2015-09-10 03:57 ./usr/bin/vcftools
drwxr-xr-x root/root 0 2015-09-10 03:57 ./usr/share/
drwxr-xr-x root/root 0 2015-09-10 03:57 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-10 03:57 ./usr/share/doc/vcftools/
-rw-r--r-- root/root 1135 2015-08-09 07:49 ./usr/share/doc/vcftools/changelog.Debian.gz
-rw-r--r-- root/root 1961 2015-07-08 20:54 ./usr/share/doc/vcftools/changelog.gz
-rw-r--r-- root/root 1154 2015-08-09 07:50 ./usr/share/doc/vcftools/copyright
drwxr-xr-x root/root 0 2015-09-10 03:57 ./usr/share/doc/vcftools/examples/
-rw-r--r-- root/root 1685 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/annotate-test.vcf
-rw-r--r-- root/root 1376 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/annotate.out
-rw-r--r-- root/root 299 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/annotate.txt
-rw-r--r-- root/root 3107 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/annotate2.out
-rw-r--r-- root/root 1394 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/annotate3.out
-rw-r--r-- root/root 522 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/cmp-test-a-3.3.vcf
-rw-r--r-- root/root 638 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/cmp-test-a.vcf
-rw-r--r-- root/root 520 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/cmp-test-b-3.3.vcf
-rw-r--r-- root/root 636 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/cmp-test-b.vcf
-rw-r--r-- root/root 2633 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/cmp-test.out
-rw-r--r-- root/root 1180 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/concat-a.vcf
-rw-r--r-- root/root 674 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/concat-b.vcf
-rw-r--r-- root/root 972 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/concat-c.vcf
-rw-r--r-- root/root 2074 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/concat.out
-rw-r--r-- root/root 1038 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/consensus.fa
-rw-r--r-- root/root 1037 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/consensus.out
-rw-r--r-- root/root 1037 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/consensus.out2
-rw-r--r-- root/root 275 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/consensus.vcf
-rw-r--r-- root/root 2312 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/contrast.out.gz
-rw-r--r-- root/root 8723 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/contrast.vcf.gz
-rw-r--r-- root/root 1524 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/fill-an-ac.out
-rw-r--r-- root/root 1800 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/filters.txt.gz
-rw-r--r-- root/root 1924 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/fix-ploidy.out
-rw-r--r-- root/root 42 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/fix-ploidy.samples
-rw-r--r-- root/root 223 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/fix-ploidy.txt
-rw-r--r-- root/root 3335 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/fix-ploidy.vcf.gz
-rw-r--r-- root/root 564 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/floats.vcf
-rw-r--r-- root/root 48 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/indel-stats.out
-rw-r--r-- root/root 24 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/indel-stats.tab
-rw-r--r-- root/root 523 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/indel-stats.vcf
-rw-r--r-- root/root 2086 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/invalid-4.0.vcf
-rw-r--r-- root/root 1120 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/isec-n2-test.vcf.out
-rw-r--r-- root/root 965 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/merge-test-a.vcf
-rw-r--r-- root/root 1020 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/merge-test-b.vcf
-rw-r--r-- root/root 798 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/merge-test-c.vcf
-rw-r--r-- root/root 2240 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/merge-test.vcf.out
-rw-r--r-- root/root 230 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/parse-test.vcf
-rw-r--r-- root/root 1439 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/perl-api-1.pl
-rw-r--r-- root/root 255 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/query-test.out
-rw-r--r-- root/root 638 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/shuffle-test.vcf
-rw-r--r-- root/root 522 2015-07-08 20:54 ./usr/share/doc/vcftools/examples/subset.SNPs.out
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 51172
Build-Time: 620
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 149
Job: vcftools_0.1.13+dfsg-1
Machine Architecture: armhf
Package: vcftools
Package-Time: 825
Source-Version: 0.1.13+dfsg-1
Space: 51172
Status: successful
Version: 0.1.13+dfsg-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150910-0358
Build needed 00:13:45, 51172k disc space