vcftools →
0.1.14+dfsg-4+deb9u1 →
armhf → 2019-04-27 11:18:19
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| vcftools 0.1.14+dfsg-4+deb9u1 (armhf) Sat, 27 Apr 2019 11:05:41 +0000 |
+==============================================================================+
Package: vcftools
Version: 0.1.14+dfsg-4+deb9u1
Source Version: 0.1.14+dfsg-4+deb9u1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-fd5179a5-edb6-464f-afd4-388aa46f9016' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9719 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 28s (750 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'vcftools' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/vcftools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/vcftools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 206 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main vcftools 0.1.14+dfsg-4+deb9u1 (dsc) [2164 B]
Get:2 http://172.17.0.1/private stretch-staging/main vcftools 0.1.14+dfsg-4+deb9u1 (tar) [190 kB]
Get:3 http://172.17.0.1/private stretch-staging/main vcftools 0.1.14+dfsg-4+deb9u1 (diff) [13.9 kB]
Fetched 206 kB in 0s (3825 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/vcftools-Ntpn43/vcftools-0.1.14+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/vcftools-Ntpn43' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-S4ZA1j/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-S4ZA1j/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (3089 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 63 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 772 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13974 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), dh-autoreconf, pkg-config, zlib1g-dev
Filtered Build-Depends: debhelper (>= 10), dh-autoreconf, pkg-config, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-vcftools-dummy' in '/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive/sbuild-build-depends-vcftools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-vcftools-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ Sources [512 B]
Get:5 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ Packages [591 B]
Fetched 2436 B in 0s (3555 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install vcftools build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtool libunistring0 libxml2 m4 man-db
pkg-config po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtool libunistring0 libxml2 m4 man-db
pkg-config po-debconf sbuild-build-depends-vcftools-dummy zlib1g-dev
0 upgraded, 33 newly installed, 0 to remove and 63 not upgraded.
Need to get 19.3 MB/19.4 MB of archives.
After this operation, 65.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-S4ZA1j/apt_archive ./ sbuild-build-depends-vcftools-dummy 0.invalid.0 [804 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.30-1+deb9u2 [222 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.30-1+deb9u2 [105 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.30-1+deb9u2 [63.6 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-6+deb9u2 [7425 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.2+deb9u2 [806 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1+deb9u1 [96.2 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.034-1 [16.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.034-1 [10.5 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.3-2 [2527 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-3 [131 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libarchive-zip-perl (1.59-1+deb9u1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-9) ...
Setting up gettext-base (0.19.8.1-2) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6+deb9u2) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.2+deb9u2) ...
Setting up libmagic-mgc (1:5.30-1+deb9u2) ...
Setting up libmagic1:armhf (1:5.30-1+deb9u2) ...
Processing triggers for libc-bin (2.24-11) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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 autopoint (0.19.8.1-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.034-1) ...
Setting up libglib2.0-0:armhf (2.50.3-2) ...
No schema files found: doing nothing.
Setting up autoconf (2.69-10) ...
Setting up file (1:5.30-1+deb9u2) ...
Setting up libcroco3:armhf (0.6.11-3) ...
Setting up pkg-config (0.29-4) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up gettext (0.19.8.1-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.034-1) ...
Setting up debhelper (10.2.5) ...
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Processing triggers for libc-bin (2.24-11) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-5 dpkg-dev_1.18.24 g++-6_6.3.0-18+rpi1 gcc-6_6.3.0-18+rpi1 libc6-dev_2.24-11 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.4.6 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.9+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-5 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4 cpp-6_6.3.0-18+rpi1 dash_0.5.8-2.4 debconf_1.5.61 debfoster_2.7-2.1 debhelper_10.2.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.034-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1+deb9u2 findutils_4.6.0+git+20161106-2 fuse2fs_1.43.4-2 g++_4:6.3.0-4 g++-6_6.3.0-18+rpi1 gcc_4:6.3.0-4 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.3.0-18+rpi1 gcc-6-base_6.3.0-18+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gnupg_2.1.18-6 gnupg-agent_2.1.18-6 gnupg-l10n_2.1.18-6 gpgv_2.1.18-6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init_1.48 init-system-helpers_1.48 initscripts_2.88dsf-59.9 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libapparmor1_2.11.0-3 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.4.6 libarchive-zip-perl_1.59-1+deb9u1 libasan1_4.9.3-14 libasan3_6.3.0-18+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-18+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-2 libaudit1_1:2.6.7-2 libblkid1_2.29.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-11 libc-dev-bin_2.24-11 libc6_2.24-11 libc6-dev_2.24-11 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.3.0-18+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.3-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.18-1 libdebconfclient0_0.227 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.74-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.034-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.3.0-18+rpi1 libgcc1_1:6.3.0-18+rpi1 libgcrypt20_1.7.6-2 libgdbm3_1.8.3-14 libglib2.0-0_2.50.3-2 libgmp10_2:6.1.2+dfsg-1 libgomp1_6.3.0-18+rpi1 libgpg-error0_1.26-2 libicu57_57.1-6+deb9u2 libidn11_1.33-1 libip4tc0_1.6.0+snapshot20161117-6 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_23-2 libksba8_1.3.5-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1+deb9u2 libmagic1_1:5.30-1+deb9u2 libmount1_2.29.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnpth0_1.3-1 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-3 libreadline7_7.0-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 libsystemd0_232-25 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libubsan0_6.3.0-18+rpi1 libudev1_232-25 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-2.2+deb9u2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.10-2 mawk_1.3.3-17 mount_2.29.2-1 multiarch-support_2.24-11 nano_2.7.4-1 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.24.1-3 perl-base_5.24.1-3 perl-modules-5.24_5.24.1-3 pinentry-curses_1.0.0-2 pkg-config_0.29-4 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-vcftools-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-25 systemd-sysv_232-25 sysv-rc_2.88dsf-59.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2017b-1 udev_232-25 util-linux_2.29.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Apr 15 06:28:48 2019 UTC
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./vcftools_0.1.14+dfsg-4+deb9u1.dsc
dpkg-source: info: extracting vcftools in /<<BUILDDIR>>/vcftools-0.1.14+dfsg
dpkg-source: info: unpacking vcftools_0.1.14+dfsg.orig.tar.xz
dpkg-source: info: unpacking vcftools_0.1.14+dfsg-4+deb9u1.debian.tar.xz
dpkg-source: info: applying temporary_test_fix.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying manpage.patch
dpkg-source: info: applying 0001-vcf-fix-ploidy-make-p-work-without-.-on-INC.patch
dpkg-source: info: applying CVE-2018-11099_CVE-2018-11129_CVE-2018-11130.patch
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
LC_ALL=POSIX
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-fd5179a5-edb6-464f-afd4-388aa46f9016
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package vcftools
dpkg-buildpackage: info: source version 0.1.14+dfsg-4+deb9u1
dpkg-buildpackage: info: source distribution stretch
dpkg-source --before-build vcftools-0.1.14+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
dh_clean
rm -f debian/debhelper-build-stamp
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
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + > debian/autoreconf.before
autoreconf -f -i
configure.ac:16: installing './compile'
configure.ac:12: installing './install-sh'
configure.ac:12: installing './missing'
src/cpp/Makefile.am: installing './depcomp'
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + > debian/autoreconf.after
rm -f debian/*.debhelper.log
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
dh_auto_configure -- --with-pmdir=/usr/share/perl5
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --with-pmdir=/usr/share/perl5
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ZLIB... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for int8_t... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for error_at_line... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for gethostbyaddr... yes
checking for gethostbyname... yes
checking for memset... yes
checking for pow... no
checking for select... yes
checking for socket... yes
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... yes
checking for strstr... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/cpp/Makefile
config.status: creating src/perl/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
make[1]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
Making all in src
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
Making all in cpp
make[4]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp
gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`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++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp
In file included from /usr/include/c++/6/vector:69:0,
from entry.h:12,
from bcf_entry.h:10,
from bcf_entry_setters.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from entry.h:12,
from bcf_entry.h:10,
from bcf_entry_setters.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void bcf_entry::set_indv_GQUALITY(unsigned int, const float&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'void bcf_entry::set_indv_GQUALITY(unsigned int, const std::vector<char>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp
gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c
In file included from knetfile.c:46:0:
knetfile.c: In function 'kftp_send_cmd':
knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^~~~~~~~~~~~~~~~~~~
knetfile.c:236:2: note: in expansion of macro 'netwrite'
netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
^~~~~~~~
knetfile.c: In function 'khttp_connect_file':
knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^~~~~~~~~~~~~~~~~~~
knetfile.c:415:2: note: in expansion of macro 'netwrite'
netwrite(fp->fd, buf, l);
^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp
In file included from /usr/include/c++/6/vector:69:0,
from entry.h:12,
from vcf_entry.h:12,
from vcf_entry_setters.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from entry.h:12,
from vcf_entry.h:12,
from vcf_entry_setters.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void vcf_entry::set_indv_GQUALITY(unsigned int, double)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp
In file included from /usr/include/c++/6/vector:69:0,
from variant_file.h:35,
from variant_file_output.cpp:8:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = std::pair<int, double>; _Alloc = std::allocator<std::pair<int, double> >]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<std::pair<int, double> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from variant_file.h:35,
from variant_file_output.cpp:8:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void variant_file::output_Tajima_D(const parameters&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vcftools-0.1.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz
make[4]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/cpp'
Making all in perl
make[4]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/perl'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/perl'
make[4]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
Making check in cpp
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/cpp'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/cpp'
Making check in perl
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/perl'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/perl'
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
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 -j4 install DESTDIR=/<<BUILDDIR>>/vcftools-0.1.14\+dfsg/debian/vcftools AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
Making install in src
make[2]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
Making install in cpp
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/cpp'
make[4]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/cpp'
/bin/mkdir -p '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/man/man1'
/usr/bin/install -c vcftools '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/bin'
/usr/bin/install -c -m 644 vcftools.1 '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/man/man1'
make[4]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/cpp'
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/cpp'
Making install in perl
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/perl'
make[4]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/perl'
/bin/mkdir -p '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/perl5'
/usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/perl5'
/usr/bin/install -c fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/bin'
make[4]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/perl'
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src/perl'
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
dh_installdocs -a
install -d debian/vcftools/usr/share/doc/vcftools
cp --reflink=auto -a debian/README.test debian/vcftools/usr/share/doc/vcftools
cp --reflink=auto -a debian/tests/run-unit-test debian/vcftools/usr/share/doc/vcftools
chown -R 0:0 debian/vcftools/usr/share/doc
chmod -R go=rX debian/vcftools/usr/share/doc
chmod -R u\+rw debian/vcftools/usr/share/doc
install -p -m0644 debian/copyright debian/vcftools/usr/share/doc/vcftools/copyright
rm -f debian/*.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
dh_installchangelogs src/perl/ChangeLog
install -p -m0644 debian/changelog debian/vcftools/usr/share/doc/vcftools/changelog.Debian
install -p -m0644 src/perl/ChangeLog debian/vcftools/usr/share/doc/vcftools/changelog
make[1]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
rm -f debian/*.debhelper.log
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
dh_installexamples;
mkdir -p /<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/doc/vcftools/examples/testsuite;
mkdir -p /<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/doc/vcftools/examples/testdata;
cp ./examples/* /<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/doc/vcftools/examples/testdata/;
find ./src/perl/ \( -name "*.pm" -o -name "*fill*" -o -name "test.t" \) -exec cp \{\} /<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/doc/vcftools/examples/testsuite \;
sed -i 's#examples#testdata#g' /<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t;
sed -i 's#I\.\./perl/#I\.\./\.#g' /<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t;
sed -i 's#\.\./perl/#/usr/bin/#g' /<<BUILDDIR>>/vcftools-0.1.14+dfsg/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t;
make[1]: Leaving directory '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
dh_installman -a
install -p -m0644 debian/mans/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-aa.1
install -p -m0644 debian/mans/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1
install -p -m0644 debian/mans/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-fs.1
install -p -m0644 debian/mans/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1
install -p -m0644 debian/mans/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1
install -p -m0644 debian/mans/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1
install -p -m0644 debian/mans/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-compare.1
install -p -m0644 debian/mans/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-concat.1
install -p -m0644 debian/mans/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1
install -p -m0644 debian/mans/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1
install -p -m0644 debian/mans/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-convert.1
install -p -m0644 debian/mans/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1
install -p -m0644 debian/mans/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1
install -p -m0644 debian/mans/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1
install -p -m0644 debian/mans/vcf-isec.1 debian/vcftools/usr/share/man/man1/vcf-isec.1
install -p -m0644 debian/mans/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-merge.1
install -p -m0644 debian/mans/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1
install -p -m0644 debian/mans/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-query.1
install -p -m0644 debian/mans/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1
install -p -m0644 debian/mans/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-sort.1
install -p -m0644 debian/mans/vcf-stats.1 debian/vcftools/usr/share/man/man1/vcf-stats.1
install -p -m0644 debian/mans/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-subset.1
install -p -m0644 debian/mans/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1
install -p -m0644 debian/mans/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1
install -p -m0644 debian/mans/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcf-validator.1
install -p -m0644 src/cpp/vcftools.1 debian/vcftools/usr/share/man/man1/vcftools.1
man --recode UTF-8 ./fill\-aa\.1 > fill\-aa\.1\.new
chmod 0755 -- fill-aa.1.new
chown 0:0 -- 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 0755 -- fill-an-ac.1.new
chown 0:0 -- fill-an-ac.1.new
mv -f fill-an-ac.1.new fill-an-ac.1
man --recode UTF-8 ./fill\-fs\.1 > fill\-fs\.1\.new
chmod 0755 -- fill-fs.1.new
chown 0:0 -- 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 0755 -- fill-ref-md5.1.new
chown 0:0 -- fill-ref-md5.1.new
mv -f fill-ref-md5.1.new fill-ref-md5.1
man --recode UTF-8 ./fill\-rsIDs\.1 > fill\-rsIDs\.1\.new
chmod 0755 -- fill-rsIDs.1.new
chown 0:0 -- fill-rsIDs.1.new
mv -f fill-rsIDs.1.new fill-rsIDs.1
man --recode UTF-8 ./vcf\-annotate\.1 > vcf\-annotate\.1\.new
chmod 0755 -- vcf-annotate.1.new
chown 0:0 -- 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 0755 -- vcf-compare.1.new
chown 0:0 -- 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 0755 -- vcf-concat.1.new
chown 0:0 -- vcf-concat.1.new
mv -f vcf-concat.1.new vcf-concat.1
man --recode UTF-8 ./vcf\-consensus\.1 > vcf\-consensus\.1\.new
chmod 0755 -- vcf-consensus.1.new
chown 0:0 -- 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 0755 -- vcf-contrast.1.new
chown 0:0 -- vcf-contrast.1.new
mv -f vcf-contrast.1.new vcf-contrast.1
man --recode UTF-8 ./vcf\-convert\.1 > vcf\-convert\.1\.new
chmod 0755 -- vcf-convert.1.new
chown 0:0 -- vcf-convert.1.new
mv -f vcf-convert.1.new vcf-convert.1
man --recode UTF-8 ./vcf\-fix\-newlines\.1 > vcf\-fix\-newlines\.1\.new
chmod 0755 -- vcf-fix-newlines.1.new
chown 0:0 -- vcf-fix-newlines.1.new
mv -f vcf-fix-newlines.1.new vcf-fix-newlines.1
man --recode UTF-8 ./vcf\-fix\-ploidy\.1 > vcf\-fix\-ploidy\.1\.new
chmod 0755 -- vcf-fix-ploidy.1.new
chown 0:0 -- 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 0755 -- vcf-indel-stats.1.new
chown 0:0 -- vcf-indel-stats.1.new
mv -f vcf-indel-stats.1.new vcf-indel-stats.1
man --recode UTF-8 ./vcf\-isec\.1 > vcf\-isec\.1\.new
chmod 0755 -- vcf-isec.1.new
chown 0:0 -- 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 0755 -- vcf-merge.1.new
chown 0:0 -- vcf-merge.1.new
mv -f vcf-merge.1.new vcf-merge.1
man --recode UTF-8 ./vcf\-phased\-join\.1 > vcf\-phased\-join\.1\.new
chmod 0755 -- vcf-phased-join.1.new
chown 0:0 -- vcf-phased-join.1.new
mv -f vcf-phased-join.1.new vcf-phased-join.1
man --recode UTF-8 ./vcf\-query\.1 > vcf\-query\.1\.new
chmod 0755 -- vcf-query.1.new
chown 0:0 -- vcf-query.1.new
mv -f vcf-query.1.new vcf-query.1
man --recode UTF-8 ./vcf\-shuffle\-cols\.1 > vcf\-shuffle\-cols\.1\.new
chmod 0755 -- vcf-shuffle-cols.1.new
chown 0:0 -- vcf-shuffle-cols.1.new
mv -f vcf-shuffle-cols.1.new vcf-shuffle-cols.1
man --recode UTF-8 ./vcf\-sort\.1 > vcf\-sort\.1\.new
chmod 0755 -- vcf-sort.1.new
chown 0:0 -- 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 0755 -- vcf-stats.1.new
chown 0:0 -- 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 0755 -- vcf-subset.1.new
chown 0:0 -- 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 0755 -- vcf-to-tab.1.new
chown 0:0 -- vcf-to-tab.1.new
mv -f vcf-to-tab.1.new vcf-to-tab.1
man --recode UTF-8 ./vcf\-tstv\.1 > vcf\-tstv\.1\.new
chmod 0755 -- vcf-tstv.1.new
chown 0:0 -- vcf-tstv.1.new
mv -f vcf-tstv.1.new vcf-tstv.1
man --recode UTF-8 ./vcf\-validator\.1 > vcf\-validator\.1\.new
chmod 0755 -- vcf-validator.1.new
chown 0:0 -- vcf-validator.1.new
mv -f vcf-validator.1.new vcf-validator.1
man --recode UTF-8 ./vcftools\.1 > vcftools\.1\.new
chmod 0755 -- vcftools.1.new
chown 0:0 -- vcftools.1.new
mv -f vcftools.1.new vcftools.1
dh_perl -a
(grep -a -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_strip_nondeterminism -a
dh_compress -a
cd debian/vcftools
chmod a-x usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/doc/vcftools/examples/testdata/contrast.out usr/share/doc/vcftools/examples/testdata/contrast.vcf usr/share/doc/vcftools/examples/testdata/filters.txt usr/share/doc/vcftools/examples/testdata/fix-ploidy.vcf usr/share/doc/vcftools/examples/testdata/valid-4.0.vcf.stats usr/share/doc/vcftools/examples/testsuite/FaSlice.pm usr/share/doc/vcftools/examples/testsuite/Vcf.pm usr/share/doc/vcftools/examples/testsuite/VcfStats.pm usr/share/doc/vcftools/examples/testsuite/fill-aa usr/share/doc/vcftools/examples/testsuite/fill-fs usr/share/doc/vcftools/examples/testsuite/fill-ref-md5 usr/share/doc/vcftools/examples/testsuite/test.t usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.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-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.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-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1
gzip -9nf usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/doc/vcftools/examples/testdata/contrast.out usr/share/doc/vcftools/examples/testdata/contrast.vcf usr/share/doc/vcftools/examples/testdata/filters.txt usr/share/doc/vcftools/examples/testdata/fix-ploidy.vcf usr/share/doc/vcftools/examples/testdata/valid-4.0.vcf.stats usr/share/doc/vcftools/examples/testsuite/FaSlice.pm usr/share/doc/vcftools/examples/testsuite/Vcf.pm usr/share/doc/vcftools/examples/testsuite/VcfStats.pm usr/share/doc/vcftools/examples/testsuite/fill-aa usr/share/doc/vcftools/examples/testsuite/fill-fs usr/share/doc/vcftools/examples/testsuite/fill-ref-md5 usr/share/doc/vcftools/examples/testsuite/test.t usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.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-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.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-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1
cd '/<<BUILDDIR>>/vcftools-0.1.14+dfsg'
dh_fixperms -a
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 -type f -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/usr/lib/arm-linux-gnueabihf/perl5/5.24 debian/vcftools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/vcftools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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
dh_strip -a
install -d debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/41
objcopy --only-keep-debug --compress-debug-sections debian/vcftools/usr/bin/vcftools debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/41/78953cc82b2ca8b3e1077b8fab78ddd4311a33.debug
chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/41/78953cc82b2ca8b3e1077b8fab78ddd4311a33.debug
chown 0:0 -- debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/41/78953cc82b2ca8b3e1077b8fab78ddd4311a33.debug
strip --remove-section=.comment --remove-section=.note debian/vcftools/usr/bin/vcftools
objcopy --add-gnu-debuglink debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/41/78953cc82b2ca8b3e1077b8fab78ddd4311a33.debug debian/vcftools/usr/bin/vcftools
install -d debian/.debhelper/vcftools/dbgsym-root/usr/share/doc
ln -s vcftools debian/.debhelper/vcftools/dbgsym-root/usr/share/doc/vcftools-dbgsym
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
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/vcftools/usr/bin/vcftools was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
echo misc:Depends= >> debian/vcftools.substvars
echo misc:Pre-Depends= >> debian/vcftools.substvars
install -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN
dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -Pdebian/.debhelper/vcftools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=vcftools-dbgsym "-DDepends=vcftools (= \${binary:Version})" "-DDescription=Debug symbols for vcftools" -DBuild-Ids=4178953cc82b2ca8b3e1077b8fab78ddd4311a33 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -Pdebian/vcftools
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 | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/vcftools/DEBIAN/md5sums
chown 0:0 -- debian/vcftools/DEBIAN/md5sums
(cd debian/.debhelper/vcftools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/vcftools/dbgsym-root ..
dpkg-deb: building package 'vcftools-dbgsym' in '../vcftools-dbgsym_0.1.14+dfsg-4+deb9u1_armhf.deb'.
dpkg-deb --build debian/vcftools ..
dpkg-deb: building package 'vcftools' in '../vcftools_0.1.14+dfsg-4+deb9u1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../vcftools_0.1.14+dfsg-4+deb9u1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build vcftools-0.1.14+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-04-27T11:18:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
vcftools_0.1.14+dfsg-4+deb9u1_armhf.changes:
--------------------------------------------
Format: 1.8
Date: Sun, 14 Apr 2019 17:49:29 +0200
Source: vcftools
Binary: vcftools
Architecture: armhf
Version: 0.1.14+dfsg-4+deb9u1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
vcftools - Collection of tools to work with VCF files
Closes: 902190
Changes:
vcftools (0.1.14+dfsg-4+deb9u1) stretch; urgency=medium
.
* Team upload.
* Add patch from upstream to fix CVE-2018-11099, CVE-2018-11129 and
CVE-2018-11130 (Closes: #902190).
Checksums-Sha1:
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5b44492d92910ce091e49727875db52b759fa8fd 4607 vcftools_0.1.14+dfsg-4+deb9u1_armhf.buildinfo
88dfdcd0430e6d38530146fe25dcd8ab126b275a 399744 vcftools_0.1.14+dfsg-4+deb9u1_armhf.deb
Checksums-Sha256:
caca45349f80400efa806d5ae69c948bd74414feb3fe76558590a03e9a3e5cbf 3446038 vcftools-dbgsym_0.1.14+dfsg-4+deb9u1_armhf.deb
c0cf9ad2451782057299f08113a999c94d9106ab685997fdf68527acab3a1627 4607 vcftools_0.1.14+dfsg-4+deb9u1_armhf.buildinfo
c646e5313d01c694d13b5a255ce3f2a39f2139348c47bbab00de00867dfdc6fb 399744 vcftools_0.1.14+dfsg-4+deb9u1_armhf.deb
Files:
fce52eab0257d5b5c22f06ace0213f7f 3446038 debug extra vcftools-dbgsym_0.1.14+dfsg-4+deb9u1_armhf.deb
b627bbfb85dc4b746ce93ea87fec8297 4607 science optional vcftools_0.1.14+dfsg-4+deb9u1_armhf.buildinfo
d236d9dab258d1ee59de126455c846b3 399744 science optional vcftools_0.1.14+dfsg-4+deb9u1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
vcftools-dbgsym_0.1.14+dfsg-4+deb9u1_armhf.deb
----------------------------------------------
new debian package, version 2.0.
size 3446038 bytes: control archive=493 bytes.
436 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: vcftools-dbgsym
Source: vcftools
Version: 0.1.14+dfsg-4+deb9u1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3476
Depends: vcftools (= 0.1.14+dfsg-4+deb9u1)
Section: debug
Priority: extra
Homepage: https://vcftools.github.io/
Description: Debug symbols for vcftools
Build-Ids: 4178953cc82b2ca8b3e1077b8fab78ddd4311a33
drwxr-xr-x root/root 0 2019-04-14 15:49 ./
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/lib/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/lib/debug/.build-id/41/
-rw-r--r-- root/root 3549052 2019-04-14 15:49 ./usr/lib/debug/.build-id/41/78953cc82b2ca8b3e1077b8fab78ddd4311a33.debug
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/share/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-04-14 15:49 ./usr/share/doc/vcftools-dbgsym -> vcftools
vcftools_0.1.14+dfsg-4+deb9u1_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 399744 bytes: control archive=3760 bytes.
696 bytes, 15 lines control
8655 bytes, 114 lines md5sums
Package: vcftools
Version: 0.1.14+dfsg-4+deb9u1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1275
Depends: libc6 (>= 2.15), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.6), perl
Recommends: tabix
Section: science
Priority: optional
Homepage: https://vcftools.github.io/
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 2019-04-14 15:49 ./
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/bin/
-rwxr-xr-x root/root 6104 2019-04-14 15:49 ./usr/bin/fill-aa
-rwxr-xr-x root/root 1261 2019-04-14 15:49 ./usr/bin/fill-an-ac
-rwxr-xr-x root/root 8068 2019-04-14 15:49 ./usr/bin/fill-fs
-rwxr-xr-x root/root 6567 2019-04-14 15:49 ./usr/bin/fill-ref-md5
-rwxr-xr-x root/root 51253 2019-04-14 15:49 ./usr/bin/vcf-annotate
-rwxr-xr-x root/root 57390 2019-04-14 15:49 ./usr/bin/vcf-compare
-rwxr-xr-x root/root 10952 2019-04-14 15:49 ./usr/bin/vcf-concat
-rwxr-xr-x root/root 9226 2019-04-14 15:49 ./usr/bin/vcf-consensus
-rwxr-xr-x root/root 8797 2019-04-14 15:49 ./usr/bin/vcf-contrast
-rwxr-xr-x root/root 6176 2019-04-14 15:49 ./usr/bin/vcf-convert
-rwxr-xr-x root/root 2298 2019-04-14 15:49 ./usr/bin/vcf-fix-newlines
-rwxr-xr-x root/root 10815 2019-04-14 15:49 ./usr/bin/vcf-fix-ploidy
-rwxr-xr-x root/root 4376 2019-04-14 15:49 ./usr/bin/vcf-indel-stats
-rwxr-xr-x root/root 21173 2019-04-14 15:49 ./usr/bin/vcf-isec
-rwxr-xr-x root/root 22988 2019-04-14 15:49 ./usr/bin/vcf-merge
-rwxr-xr-x root/root 23234 2019-04-14 15:49 ./usr/bin/vcf-phased-join
-rwxr-xr-x root/root 15832 2019-04-14 15:49 ./usr/bin/vcf-query
-rwxr-xr-x root/root 2301 2019-04-14 15:49 ./usr/bin/vcf-shuffle-cols
-rwxr-xr-x root/root 3310 2019-04-14 15:49 ./usr/bin/vcf-sort
-rwxr-xr-x root/root 4874 2019-04-14 15:49 ./usr/bin/vcf-stats
-rwxr-xr-x root/root 7706 2019-04-14 15:49 ./usr/bin/vcf-subset
-rwxr-xr-x root/root 2543 2019-04-14 15:49 ./usr/bin/vcf-to-tab
-rwxr-xr-x root/root 1820 2019-04-14 15:49 ./usr/bin/vcf-tstv
-rwxr-xr-x root/root 3353 2019-04-14 15:49 ./usr/bin/vcf-validator
-rwxr-xr-x root/root 673344 2019-04-14 15:49 ./usr/bin/vcftools
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/share/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/share/doc/vcftools/
-rw-r--r-- root/root 261 2019-04-14 15:49 ./usr/share/doc/vcftools/README.test
-rw-r--r-- root/root 1679 2019-04-14 15:49 ./usr/share/doc/vcftools/changelog.Debian.gz
-rw-r--r-- root/root 1961 2015-09-15 18:04 ./usr/share/doc/vcftools/changelog.gz
-rw-r--r-- root/root 1154 2019-04-14 15:49 ./usr/share/doc/vcftools/copyright
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/
drwxr-xr-x root/root 0 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/
-rw-r--r-- root/root 1685 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/annotate-test.vcf
-rw-r--r-- root/root 1376 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/annotate.out
-rw-r--r-- root/root 299 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/annotate.txt
-rw-r--r-- root/root 3107 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/annotate2.out
-rw-r--r-- root/root 1394 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/annotate3.out
-rw-r--r-- root/root 522 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/cmp-test-a-3.3.vcf
-rw-r--r-- root/root 638 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/cmp-test-a.vcf
-rw-r--r-- root/root 520 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/cmp-test-b-3.3.vcf
-rw-r--r-- root/root 636 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/cmp-test-b.vcf
-rw-r--r-- root/root 2633 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/cmp-test.out
-rw-r--r-- root/root 1180 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/concat-a.vcf
-rw-r--r-- root/root 674 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/concat-b.vcf
-rw-r--r-- root/root 972 2019-04-14 15:49 ./usr/share/doc/vcftools/examples/testdata/concat-c.vcf
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 43500
Build-Time: 371
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 330
Job: vcftools_0.1.14+dfsg-4+deb9u1
Machine Architecture: armhf
Package: vcftools
Package-Time: 751
Source-Version: 0.1.14+dfsg-4+deb9u1
Space: 43500
Status: successful
Version: 0.1.14+dfsg-4+deb9u1
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Finished at 2019-04-27T11:18:12Z
Build needed 00:12:31, 43500k disc space