vcftools →
0.1.16-2 →
armhf → 2020-11-19 09:56:36
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| vcftools 0.1.16-2 (armhf) Thu, 19 Nov 2020 09:42:07 +0000 |
+==============================================================================+
Package: vcftools
Version: 0.1.16-2
Source Version: 0.1.16-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-a712826a-a80b-4f2b-8162-a68b7236d382' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.8 MB in 25s (975 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://salsa.debian.org/med-team/vcftools.git
Please use:
git clone https://salsa.debian.org/med-team/vcftools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 261 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main vcftools 0.1.16-2 (dsc) [2071 B]
Get:2 http://172.17.0.1/private bullseye-staging/main vcftools 0.1.16-2 (tar) [245 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main vcftools 0.1.16-2 (diff) [13.9 kB]
Fetched 261 kB in 0s (1402 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/vcftools-z8gwjt/vcftools-0.1.16' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/vcftools-z8gwjt' 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-MULTUm/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-MULTUm/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-MULTUm/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-MULTUm/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2694 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:
bsdextrautils krb5-locales libpam-cap netbase sensible-utils
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 31 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12766 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-compat (= 13), pkg-config, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 13), pkg-config, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-vcftools-dummy' in '/<<BUILDDIR>>/resolver-MULTUm/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-MULTUm/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ Sources [508 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ Packages [588 B]
Fetched 2429 B in 1s (3130 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:
krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db pkg-config po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-vcftools-dummy
zlib1g-dev
0 upgraded, 34 newly installed, 0 to remove and 31 not upgraded.
Need to get 18.7 MB of archives.
After this operation, 68.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-MULTUm/apt_archive ./ sbuild-build-depends-vcftools-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.2-1 [1176 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.2 [578 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libicu67:armhf (67.1-4) ...
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Setting up libglib2.0-0:armhf (2.66.2-1) ...
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Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up pkg-config (0.29.2-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
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Setting up libelf1:armhf (0.182-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.2) ...
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Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (13.2.1) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-vcftools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
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_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-13+rpi1 gcc-10_10.2.0-13+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc1-2 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-13+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-13+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-13+rpi1 gcc-10-base_10.2.0-13+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b1 gcc-8-base_8.4.0-4+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.17-10 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-13+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-7 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.0-13+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13+rpi1 libgcc-s1_10.2.0-13+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.2-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-13+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 libldap-2.4-2_2.4.53+dfsg-1+rpi1 libldap-common_2.4.53+dfsg-1+rpi1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.4-1+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-13+rpi1 libuchardet0_0.0.7-1 libudev1_246.4-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.2 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-vcftools-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.eyJxRshM/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 16 20:49:02 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./vcftools_0.1.16-2.dsc
dpkg-source: info: extracting vcftools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking vcftools_0.1.16.orig.tar.gz
dpkg-source: info: unpacking vcftools_0.1.16-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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
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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-a712826a-a80b-4f2b-8162-a68b7236d382
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 0.1.16-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/vcftools.substvars debian/files
rm -fr -- debian/vcftools/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -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 \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary-arch
dh binary-arch
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 {} + -o -type l -printf "symlink %p
" > debian/autoreconf.before
grep -q ^XDT_ configure.ac
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 {} + -o -type l -printf "symlink %p
" > debian/autoreconf.after
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --with-pmdir=/share/perl5
install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-pmdir=/share/perl5
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 whether make supports the include directive... yes (GNU style)
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
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
Making all in cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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]
60 | #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bgzf.c:622:2: note: in expansion of macro '_bgzf_read'
622 | _bgzf_read(fp->fp, buf, 28);
| ^~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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++/10/vector:72,
from entry.h:12,
from bcf_entry.h:10,
from bcf_entry_setters.cpp:9:
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp
In file included from /usr/include/c++/10/vector:67,
from entry.h:12,
from bcf_entry.h:10,
from bcf_entry_setters.cpp:9:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void bcf_entry::set_indv_GQUALITY(unsigned int, const float&)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void bcf_entry::set_indv_GQUALITY(unsigned int, const std::vector<char>&)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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:
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]
9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
| ^~~~~~~~~~~~~~~~~~~
knetfile.c:236:2: note: in expansion of macro 'netwrite'
236 | 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]
9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
| ^~~~~~~~~~~~~~~~~~~
knetfile.c:415:2: note: in expansion of macro 'netwrite'
415 | netwrite(fp->fd, buf, l);
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/10/vector:72,
from entry.h:12,
from vcf_entry.h:12,
from vcf_entry_setters.cpp:9:
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from entry.h:12,
from vcf_entry.h:12,
from vcf_entry_setters.cpp:9:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void vcf_entry::set_indv_GQUALITY(unsigned int, double)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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++/10/vector:72,
from variant_file.h:35,
from variant_file_output.cpp:8:
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<std::pair<int, double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<double, double>}; _Tp = std::pair<double, double>; _Alloc = std::allocator<std::pair<double, double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<double, double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, double>}; _Tp = std::pair<double, double>; _Alloc = std::allocator<std::pair<double, double> >]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/set:60,
from variant_file.h:26,
from variant_file_output.cpp:8:
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, std::pair<unsigned int, unsigned int> >; _KeyOfValue = std::_Select1st<std::pair<const double, std::pair<unsigned int, unsigned int> > >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > >]':
/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::pair<unsigned int, unsigned int> >, std::_Select1st<std::pair<const double, std::pair<unsigned int, unsigned int> > >, std::less<double>, std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > > >::const_iterator' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from variant_file.h:28,
from variant_file_output.cpp:8:
/usr/include/c++/10/bits/stl_map.h: In member function 'void variant_file::output_TsTv_by_quality(const parameters&)':
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::pair<unsigned int, unsigned int> >, std::_Select1st<std::pair<const double, std::pair<unsigned int, unsigned int> > >, std::less<double>, std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::pair<unsigned int, unsigned int> >, std::_Select1st<std::pair<const double, std::pair<unsigned int, unsigned int> > >, std::less<double>, std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from variant_file.h:35,
from variant_file_output.cpp:8:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void variant_file::output_Tajima_D(const parameters&)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/src/cpp'
Making all in perl
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/perl'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/perl'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
Making check in cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/cpp'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/cpp'
Making check in perl
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/perl'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/perl'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -fr -- /tmp/dh-xdg-rundir-G2GeN__L
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
rm -f -- debian/vcftools.substvars
rm -fr -- debian/.debhelper/generated/vcftools/ debian/vcftools/ debian/tmp/
dh_auto_install -a
install -d /<<PKGBUILDDIR>>/debian/vcftools
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/vcftools AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
Making install in cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/cpp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/cpp'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/vcftools/usr/bin'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/vcftools/usr/share/man/man1'
/usr/bin/install -c vcftools '/<<PKGBUILDDIR>>/debian/vcftools/usr/bin'
/usr/bin/install -c -m 644 vcftools.1 '/<<PKGBUILDDIR>>/debian/vcftools/usr/share/man/man1'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/cpp'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/cpp'
Making install in perl
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/perl'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/perl'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/vcftools/usr/bin'
/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/vcftools/usr/bin'
/usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/<<PKGBUILDDIR>>/debian/vcftools/usr//share/perl5'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/perl'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/perl'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/vcftools.debhelper.log
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
install -d debian/.debhelper/generated/vcftools
for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` ; do \
sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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
chmod -R u\+rw,go=rX debian/vcftools/usr/share/doc
install -p -m0644 debian/copyright debian/vcftools/usr/share/doc/vcftools/copyright
rm -f debian/vcftools.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
rm -f debian/vcftools.debhelper.log
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples;
mkdir -p /<<PKGBUILDDIR>>/debian/vcftools/usr/share/doc/vcftools/examples/testsuite;
mkdir -p /<<PKGBUILDDIR>>/debian/vcftools/usr/share/doc/vcftools/examples/testdata;
cp ./examples/* /<<PKGBUILDDIR>>/debian/vcftools/usr/share/doc/vcftools/examples/testdata/;
find ./src/perl/ \( -name "*.pm" -o -name "*fill*" -o -name "test.t" \) -exec cp \{\} /<<PKGBUILDDIR>>/debian/vcftools/usr/share/doc/vcftools/examples/testsuite \;
sed -i 's#examples#testdata#g' /<<PKGBUILDDIR>>/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t;
sed -i 's#I\.\./perl/#I\.\./\.#g' /<<PKGBUILDDIR>>/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t;
sed -i 's#\.\./perl/#/usr/bin/#g' /<<PKGBUILDDIR>>/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t;
for perlscript in `grep -lR '#!/usr/bin/env \+perl' debian/*/usr/share/doc/vcftools/examples` ; do \
sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-compare.1
man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1
man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-isec.1 debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1
man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1
mv debian/vcftools/usr/share/man/man1/vcf-subset.1.dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1
mv debian/vcftools/usr/share/man/man1/vcf-to-tab.1.dh-new debian/vcftools/usr/share/man/man1/vcf-to-tab.1
mv debian/vcftools/usr/share/man/man1/vcf-tstv.1.dh-new debian/vcftools/usr/share/man/man1/vcf-tstv.1
mv debian/vcftools/usr/share/man/man1/vcf-validator.1.dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1
mv debian/vcftools/usr/share/man/man1/vcftools.1.dh-new debian/vcftools/usr/share/man/man1/vcftools.1
chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1
mv debian/vcftools/usr/share/man/man1/vcf-concat.1.dh-new debian/vcftools/usr/share/man/man1/vcf-concat.1
mv debian/vcftools/usr/share/man/man1/vcf-consensus.1.dh-new debian/vcftools/usr/share/man/man1/vcf-consensus.1
mv debian/vcftools/usr/share/man/man1/vcf-contrast.1.dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1
mv debian/vcftools/usr/share/man/man1/vcf-convert.1.dh-new debian/vcftools/usr/share/man/man1/vcf-convert.1
mv debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1
mv debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1
mv debian/vcftools/usr/share/man/man1/vcf-indel-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-indel-stats.1
chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1
mv debian/vcftools/usr/share/man/man1/fill-aa.1.dh-new debian/vcftools/usr/share/man/man1/fill-aa.1
mv debian/vcftools/usr/share/man/man1/fill-an-ac.1.dh-new debian/vcftools/usr/share/man/man1/fill-an-ac.1
mv debian/vcftools/usr/share/man/man1/fill-fs.1.dh-new debian/vcftools/usr/share/man/man1/fill-fs.1
mv debian/vcftools/usr/share/man/man1/fill-ref-md5.1.dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1
mv debian/vcftools/usr/share/man/man1/fill-rsIDs.1.dh-new debian/vcftools/usr/share/man/man1/fill-rsIDs.1
mv debian/vcftools/usr/share/man/man1/vcf-annotate.1.dh-new debian/vcftools/usr/share/man/man1/vcf-annotate.1
mv debian/vcftools/usr/share/man/man1/vcf-compare.1.dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1
chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-compare.1
mv debian/vcftools/usr/share/man/man1/vcf-isec.1.dh-new debian/vcftools/usr/share/man/man1/vcf-isec.1
mv debian/vcftools/usr/share/man/man1/vcf-merge.1.dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1
mv debian/vcftools/usr/share/man/man1/vcf-phased-join.1.dh-new debian/vcftools/usr/share/man/man1/vcf-phased-join.1
mv debian/vcftools/usr/share/man/man1/vcf-query.1.dh-new debian/vcftools/usr/share/man/man1/vcf-query.1
mv debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1.dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1
mv debian/vcftools/usr/share/man/man1/vcf-sort.1.dh-new debian/vcftools/usr/share/man/man1/vcf-sort.1
mv debian/vcftools/usr/share/man/man1/vcf-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-stats.1
chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-isec.1 debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1
dh_perl -a
(grep -a -s -v perl:Depends debian/vcftools.substvars; echo perl:Depends=perl:any) > 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/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/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 '/<<PKGBUILDDIR>>'
dh_fixperms -a
find debian/vcftools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/vcftools/usr/share/doc -type f -a -true -a ! -regex 'debian/vcftools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/vcftools/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools/usr/share/perl5 -type f -perm -5 -name '*.pm' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a-X
find debian/vcftools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/vcftools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing -a
dh_dwz -a -a
dwz -- debian/vcftools/usr/bin/vcftools
dh_strip -a -a
install -d debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/ca
objcopy --only-keep-debug --compress-debug-sections debian/vcftools/usr/bin/vcftools debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/ca/f5a845cd30ecc19b3bc7af09bb3f8f5a737468.debug
chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/ca/f5a845cd30ecc19b3bc7af09bb3f8f5a737468.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/ca/f5a845cd30ecc19b3bc7af09bb3f8f5a737468.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 -a
rm -f debian/vcftools/DEBIAN/shlibs
dh_shlibdeps -a -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=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=vcftools-dbgsym "-DDepends=vcftools (= \${binary:Version})" "-DDescription=debug symbols for vcftools" -DBuild-Ids=caf5a845cd30ecc19b3bc7af09bb3f8f5a737468 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -Pdebian/vcftools
chmod 0644 -- debian/vcftools/DEBIAN/control
dh_md5sums -a
cd debian/vcftools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/vcftools/DEBIAN/md5sums
cd debian/.debhelper/vcftools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/vcftools ..
dpkg-deb --root-owner-group --build debian/.debhelper/vcftools/dbgsym-root ..
dpkg-deb: building package 'vcftools-dbgsym' in '../vcftools-dbgsym_0.1.16-2_armhf.deb'.
dpkg-deb: building package 'vcftools' in '../vcftools_0.1.16-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../vcftools_0.1.16-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-11-19T09:56:26Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
vcftools_0.1.16-2_armhf.changes:
--------------------------------
Format: 1.8
Date: Mon, 16 Nov 2020 18:47:17 +0100
Source: vcftools
Binary: vcftools vcftools-dbgsym
Architecture: armhf
Version: 0.1.16-2
Distribution: bullseye-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 (0.1.16-2) unstable; urgency=medium
.
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Secure URI in copyright format (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
* Remove trailing whitespace in debian/control (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
Checksums-Sha1:
ebb5cb81efb0dbf85c877622099bd7488f353acc 4909808 vcftools-dbgsym_0.1.16-2_armhf.deb
462ef54a593b9f35b9310963c24292b56be35218 5012 vcftools_0.1.16-2_armhf.buildinfo
255deda71bd3afbf4b7b1d0b1d72fd7613822379 361356 vcftools_0.1.16-2_armhf.deb
Checksums-Sha256:
e0955111f72e0b18cdf474511645220d62e06c3e26680d41a64886644605e28b 4909808 vcftools-dbgsym_0.1.16-2_armhf.deb
32ab99d71758850edbac4bf95c8f97f765074a856edb5d7680b8b11c66f0f739 5012 vcftools_0.1.16-2_armhf.buildinfo
1536b1b24ea0756b4ca40532c898f7eefca13f934ee64288e59cd79c7ba262d8 361356 vcftools_0.1.16-2_armhf.deb
Files:
f79143cb7e72fe11d58b51b58846d2a2 4909808 debug optional vcftools-dbgsym_0.1.16-2_armhf.deb
9263ae78fd2d3acb9aad607f23980512 5012 science optional vcftools_0.1.16-2_armhf.buildinfo
0e3e7e610099ce0e9b2ec8aae04af55d 361356 science optional vcftools_0.1.16-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
vcftools-dbgsym_0.1.16-2_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 4909808 bytes: control archive=536 bytes.
377 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: vcftools-dbgsym
Source: vcftools
Version: 0.1.16-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4960
Depends: vcftools (= 0.1.16-2)
Section: debug
Priority: optional
Description: debug symbols for vcftools
Build-Ids: caf5a845cd30ecc19b3bc7af09bb3f8f5a737468
drwxr-xr-x root/root 0 2020-11-16 17:47 ./
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/lib/debug/.build-id/ca/
-rw-r--r-- root/root 5067828 2020-11-16 17:47 ./usr/lib/debug/.build-id/ca/f5a845cd30ecc19b3bc7af09bb3f8f5a737468.debug
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/share/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-11-16 17:47 ./usr/share/doc/vcftools-dbgsym -> vcftools
vcftools_0.1.16-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 361356 bytes: control archive=3416 bytes.
688 bytes, 15 lines control
8619 bytes, 114 lines md5sums
Package: vcftools
Version: 0.1.16-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1485
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.6), perl:any
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 2020-11-16 17:47 ./
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/bin/
-rwxr-xr-x root/root 6100 2020-11-16 17:47 ./usr/bin/fill-aa
-rwxr-xr-x root/root 1257 2020-11-16 17:47 ./usr/bin/fill-an-ac
-rwxr-xr-x root/root 8064 2020-11-16 17:47 ./usr/bin/fill-fs
-rwxr-xr-x root/root 6563 2020-11-16 17:47 ./usr/bin/fill-ref-md5
-rwxr-xr-x root/root 51249 2020-11-16 17:47 ./usr/bin/vcf-annotate
-rwxr-xr-x root/root 57386 2020-11-16 17:47 ./usr/bin/vcf-compare
-rwxr-xr-x root/root 10948 2020-11-16 17:47 ./usr/bin/vcf-concat
-rwxr-xr-x root/root 9222 2020-11-16 17:47 ./usr/bin/vcf-consensus
-rwxr-xr-x root/root 8793 2020-11-16 17:47 ./usr/bin/vcf-contrast
-rwxr-xr-x root/root 6167 2020-11-16 17:47 ./usr/bin/vcf-convert
-rwxr-xr-x root/root 2294 2020-11-16 17:47 ./usr/bin/vcf-fix-newlines
-rwxr-xr-x root/root 10811 2020-11-16 17:47 ./usr/bin/vcf-fix-ploidy
-rwxr-xr-x root/root 4372 2020-11-16 17:47 ./usr/bin/vcf-indel-stats
-rwxr-xr-x root/root 21169 2020-11-16 17:47 ./usr/bin/vcf-isec
-rwxr-xr-x root/root 22984 2020-11-16 17:47 ./usr/bin/vcf-merge
-rwxr-xr-x root/root 23230 2020-11-16 17:47 ./usr/bin/vcf-phased-join
-rwxr-xr-x root/root 15828 2020-11-16 17:47 ./usr/bin/vcf-query
-rwxr-xr-x root/root 2297 2020-11-16 17:47 ./usr/bin/vcf-shuffle-cols
-rwxr-xr-x root/root 3306 2020-11-16 17:47 ./usr/bin/vcf-sort
-rwxr-xr-x root/root 4870 2020-11-16 17:47 ./usr/bin/vcf-stats
-rwxr-xr-x root/root 7702 2020-11-16 17:47 ./usr/bin/vcf-subset
-rwxr-xr-x root/root 2539 2020-11-16 17:47 ./usr/bin/vcf-to-tab
-rwxr-xr-x root/root 1816 2020-11-16 17:47 ./usr/bin/vcf-tstv
-rwxr-xr-x root/root 3349 2020-11-16 17:47 ./usr/bin/vcf-validator
-rwxr-xr-x root/root 718356 2020-11-16 17:47 ./usr/bin/vcftools
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/share/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/share/doc/vcftools/
-rw-r--r-- root/root 261 2020-11-16 17:47 ./usr/share/doc/vcftools/README.test
-rw-r--r-- root/root 1960 2020-11-16 17:47 ./usr/share/doc/vcftools/changelog.Debian.gz
-rw-r--r-- root/root 1961 2018-08-03 13:56 ./usr/share/doc/vcftools/changelog.gz
-rw-r--r-- root/root 1155 2020-11-16 17:47 ./usr/share/doc/vcftools/copyright
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/
drwxr-xr-x root/root 0 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/testdata/
-rw-r--r-- root/root 1685 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/testdata/annotate-test.vcf
-rw-r--r-- root/root 1376 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/testdata/annotate.out
-rw-r--r-- root/root 299 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/testdata/annotate.txt
-rw-r--r-- root/root 3107 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/testdata/annotate2.out
-rw-r--r-- root/root 1394 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/testdata/annotate3.out
-rw-r--r-- root/root 522 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/testdata/cmp-test-a-3.3.vcf
-rw-r--r-- root/root 638 2020-11-16 17:47 ./usr/share/doc/vcftools/examples/testdata/cmp-test-a.vcf
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 64072
Build-Time: 451
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 359
Job: vcftools_0.1.16-2
Machine Architecture: armhf
Package: vcftools
Package-Time: 859
Source-Version: 0.1.16-2
Space: 64072
Status: successful
Version: 0.1.16-2
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Finished at 2020-11-19T09:56:26Z
Build needed 00:14:19, 64072k disc space