I: pbuilder: network access will be disabled during build
I: Current time: Thu Apr 20 01:38:17 -12 2023
I: pbuilder-time-stamp: 1681997897
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [plink2_2.00~a3.5-220809+dfsg-1.dsc]
I: copying [./plink2_2.00~a3.5-220809+dfsg.orig.tar.xz]
I: copying [./plink2_2.00~a3.5-220809+dfsg-1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun Dec 11 20:51:20 2022 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./plink2_2.00~a3.5-220809+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting plink2 in plink2-2.00~a3.5-220809+dfsg
dpkg-source: info: unpacking plink2_2.00~a3.5-220809+dfsg.orig.tar.xz
dpkg-source: info: unpacking plink2_2.00~a3.5-220809+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying Fix_Makefile.patch
dpkg-source: info: applying use_packaged_libdeflate.patch
dpkg-source: info: applying baseline
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/20359/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
DISTRIBUTION='bookworm'
HOME='/var/lib/jenkins'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='20359'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IPBQZGqC/pbuilderrc_gyy7 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IPBQZGqC/b1 --logfile b1/build.log plink2_2.00~a3.5-220809+dfsg-1.dsc'
SUDO_GID='117'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
USERNAME='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.16:3128'
I: uname -a
Linux codethink10-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Apr 19 22:25 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/20359/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), help2man, libatlas-base-dev, liblapack-dev, libzstd-dev (>= 1.4.4), zlib1g-dev, libsimde-dev, libdeflate-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on libatlas-base-dev; however:
Package libatlas-base-dev is not installed.
pbuilder-satisfydepends-dummy depends on liblapack-dev; however:
Package liblapack-dev is not installed.
pbuilder-satisfydepends-dummy depends on libzstd-dev (>= 1.4.4); however:
Package libzstd-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsimde-dev; however:
Package libsimde-dev is not installed.
pbuilder-satisfydepends-dummy depends on libdeflate-dev; however:
Package libdeflate-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libatlas-base-dev{a} libatlas3-base{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsimde-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 42 newly installed, 0 to remove and 0 not upgraded.
Need to get 30.5 MB of archives. After unpacking 144 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main arm64 liblocale-gettext-perl arm64 1.07-5 [15.1 kB]
Get: 2 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB]
Get: 4 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB]
Get: 6 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB]
Get: 7 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 8 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB]
Get: 9 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB]
Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB]
Get: 11 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB]
Get: 12 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB]
Get: 13 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB]
Get: 14 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 16 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB]
Get: 17 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 18 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB]
Get: 19 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 25 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 26 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 27 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB]
Get: 28 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 29 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 help2man arm64 1.49.3 [198 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 libatlas3-base arm64 3.10.3-13 [2537 kB]
Get: 35 http://deb.debian.org/debian bookworm/main arm64 libatlas-base-dev arm64 3.10.3-13 [2655 kB]
Get: 36 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB]
Get: 37 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB]
Get: 38 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB]
Get: 39 http://deb.debian.org/debian bookworm/main arm64 liblapack-dev arm64 3.11.0-2 [3065 kB]
Get: 40 http://deb.debian.org/debian bookworm/main arm64 libsimde-dev all 0.7.4~rc2-2 [377 kB]
Get: 41 http://deb.debian.org/debian bookworm/main arm64 libzstd-dev arm64 1.5.4+dfsg2-5 [317 kB]
Get: 42 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB]
Fetched 30.5 MB in 1s (23.7 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package liblocale-gettext-perl.
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(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_arm64.deb ...
Unpacking liblocale-gettext-perl (1.07-5) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
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Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:arm64.
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Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../06-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
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Unpacking groff-base (1.22.4-10) ...
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Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_arm64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../09-libpipeline1_1.5.7-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.7-1) ...
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Unpacking man-db (2.11.2-2) ...
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Unpacking m4 (1.4.19-3) ...
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Unpacking libtool (2.4.7-5) ...
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Unpacking dwz (0.15-1) ...
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Unpacking libdeflate0:arm64 (1.14-1) ...
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Preparing to unpack .../36-libdeflate-dev_1.14-1_arm64.deb ...
Unpacking libdeflate-dev:arm64 (1.14-1) ...
Selecting previously unselected package liblapack3:arm64.
Preparing to unpack .../37-liblapack3_3.11.0-2_arm64.deb ...
Unpacking liblapack3:arm64 (3.11.0-2) ...
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Preparing to unpack .../38-liblapack-dev_3.11.0-2_arm64.deb ...
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Selecting previously unselected package libsimde-dev.
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Selecting previously unselected package libzstd-dev:arm64.
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Unpacking libzstd-dev:arm64 (1.5.4+dfsg2-5) ...
Selecting previously unselected package zlib1g-dev:arm64.
Preparing to unpack .../41-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ...
Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ...
Setting up libpipeline1:arm64 (1.5.7-1) ...
Setting up libsimde-dev (0.7.4~rc2-2) ...
Setting up libicu72:arm64 (72.1-3) ...
Setting up libzstd-dev:arm64 (1.5.4+dfsg2-5) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:arm64 (1:5.44-3) ...
Setting up libdeflate0:arm64 (1.14-1) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-12) ...
Setting up libgfortran5:arm64 (12.2.0-14) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:arm64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libdeflate-dev:arm64 (1.14-1) ...
Setting up libelf1:arm64 (0.188-2.1) ...
Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ...
Setting up liblocale-gettext-perl (1.07-5) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libatlas3-base:arm64 (3.10.3-13) ...
update-alternatives: using /usr/lib/aarch64-linux-gnu/atlas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
update-alternatives: using /usr/lib/aarch64-linux-gnu/atlas/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
Setting up libtool (2.4.7-5) ...
Setting up libatlas-base-dev:arm64 (3.10.3-13) ...
update-alternatives: using /usr/lib/aarch64-linux-gnu/atlas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode
update-alternatives: using /usr/lib/aarch64-linux-gnu/atlas/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.3) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up liblapack3:arm64 (3.11.0-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up liblapack-dev:arm64 (3.11.0-2) ...
Setting up debhelper (13.11.4) ...
Processing triggers for libc-bin (2.36-9) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/plink2-2.00~a3.5-220809+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../plink2_2.00~a3.5-220809+dfsg-1_source.changes
dpkg-buildpackage: info: source package plink2
dpkg-buildpackage: info: source version 2.00~a3.5-220809+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean --sourcedirectory=build_dynamic/
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_auto_clean
cd build_dynamic && make -j8 clean
make[2]: Entering directory '/build/plink2-2.00~a3.5-220809+dfsg/build_dynamic'
rm -f *.o
rm -f plink2
rm -f pgen_compress
rm -f pgenlib.a
rm -f plink2lib.a
rm -f static_pgenlib_test
rm -f static_plink2lib_test
make[2]: Leaving directory '/build/plink2-2.00~a3.5-220809+dfsg/build_dynamic'
rm -f plink2.1
rm -f pgen_compress.1
make[1]: Leaving directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_autoreconf_clean -O--sourcedirectory=build_dynamic/
dh_clean -O--sourcedirectory=build_dynamic/
debian/rules binary
dh binary --sourcedirectory=build_dynamic/
dh_update_autotools_config -O--sourcedirectory=build_dynamic/
dh_autoreconf -O--sourcedirectory=build_dynamic/
dh_auto_configure -O--sourcedirectory=build_dynamic/
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_auto_build
cd build_dynamic && make -j8 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/plink2-2.00~a3.5-220809+dfsg/build_dynamic'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security ../include/SFMT.c -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../pgen_compress.cc -o pgen_compress""
echo cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c
cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../include/plink2_bgzf.cc ../include/plink2_bitmap.cc ../include/plink2_fmath.cc ../include/plink2_stats.cc ../include/plink2_string.cc ../include/plink2_text.cc ../include/plink2_thread.cc ../include/plink2_zstfile.cc ../plink2.cc ../plink2_adjust.cc ../plink2_cmdline.cc ../plink2_common.cc ../plink2_compress_stream.cc ../plink2_data.cc ../plink2_decompress.cc ../plink2_export.cc ../plink2_export_legacy.cc ../plink2_fasta.cc ../plink2_filter.cc ../plink2_glm.cc ../plink2_glm_linear.cc ../plink2_glm_logistic.cc ../plink2_glm_shared.cc ../plink2_help.cc ../plink2_import.cc ../plink2_import_legacy.cc ../plink2_ld.cc ../plink2_matrix.cc ../plink2_matrix_calc.cc ../plink2_merge.cc ../plink2_misc.cc ../plink2_psam.cc ../plink2_pvar.cc ../plink2_random.cc ../plink2_set.cc -c
In file included from /usr/include/c++/12/algorithm:61,
from ../include/plink2_string.h:30,
from ../plink2_cmdline.h:26,
from ../plink2_compress_stream.h:27,
from ../plink2_import.cc:19:
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1844:5,
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1932:5,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)' at ../plink2_import.cc:15040:5:
/usr/include/c++/12/bits/stl_algo.h:1849:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds]
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../plink2_import.cc: In function 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)':
../plink2_import.cc:15021:14: note: at offset 128 into object 'parse_table' of size 48
15021 | uint64_t parse_table[6];
| ^~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 ../plink2_cpu.cc -c
g++ SFMT.o plink2_base.o plink2_bits.o pgenlib_misc.o pgenlib_read.o pgenlib_write.o plink2_bgzf.o plink2_bitmap.o plink2_fmath.o plink2_stats.o plink2_string.o plink2_text.o plink2_thread.o plink2_zstfile.o plink2.o plink2_adjust.o plink2_cmdline.o plink2_common.o plink2_compress_stream.o plink2_data.o plink2_decompress.o plink2_export.o plink2_export_legacy.o plink2_fasta.o plink2_filter.o plink2_glm.o plink2_glm_linear.o plink2_glm_logistic.o plink2_glm_shared.o plink2_help.o plink2_import.o plink2_import_legacy.o plink2_ld.o plink2_matrix.o plink2_matrix_calc.o plink2_merge.o plink2_misc.o plink2_psam.o plink2_pvar.o plink2_random.o plink2_set.o plink2_cpu.o -o plink2"" -llapack -lblas -lcblas -latlas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate
make[2]: Leaving directory '/build/plink2-2.00~a3.5-220809+dfsg/build_dynamic'
help2man --no-discard-stderr --name="whole genome SNP analysis" build_dynamic//pgen_compress > pgen_compress.1
make[1]: Leaving directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_auto_test -O--sourcedirectory=build_dynamic/
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedirectory=build_dynamic/
dh_prep -O--sourcedirectory=build_dynamic/
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_install build_dynamic/plink2 usr/bin/
dh_install build_dynamic/pgen_compress usr/bin/
make[1]: Leaving directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_installdocs -O--sourcedirectory=build_dynamic/
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_installchangelogs debian/upstream.docs/upstream.changelog
make[1]: Leaving directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_installexamples -O--sourcedirectory=build_dynamic/
debian/rules override_dh_installman
make[1]: Entering directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_installman debian/plink2.1
dh_installman pgen_compress.1
make[1]: Leaving directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_installsystemduser -O--sourcedirectory=build_dynamic/
dh_perl -O--sourcedirectory=build_dynamic/
dh_link -O--sourcedirectory=build_dynamic/
dh_strip_nondeterminism -O--sourcedirectory=build_dynamic/
dh_compress -O--sourcedirectory=build_dynamic/
dh_fixperms -O--sourcedirectory=build_dynamic/
dh_missing -O--sourcedirectory=build_dynamic/
dh_dwz -a -O--sourcedirectory=build_dynamic/
dh_strip -a -O--sourcedirectory=build_dynamic/
dh_makeshlibs -a -O--sourcedirectory=build_dynamic/
dh_shlibdeps -a -O--sourcedirectory=build_dynamic/
dh_installdeb -O--sourcedirectory=build_dynamic/
debian/rules override_dh_gencontrol
make[1]: Entering directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), "
make[1]: Leaving directory '/build/plink2-2.00~a3.5-220809+dfsg'
dh_md5sums -O--sourcedirectory=build_dynamic/
dh_builddeb -O--sourcedirectory=build_dynamic/
dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a3.5-220809+dfsg-1_arm64.deb'.
dpkg-deb: building package 'plink2' in '../plink2_2.00~a3.5-220809+dfsg-1_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../plink2_2.00~a3.5-220809+dfsg-1_arm64.buildinfo
dpkg-genchanges --build=binary -O../plink2_2.00~a3.5-220809+dfsg-1_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/20359 and its subdirectories
I: Current time: Thu Apr 20 01:50:13 -12 2023
I: pbuilder-time-stamp: 1681998614