plink2 →
2.00~a5.8-231123+dfsg-1 →
armhf → 2024-01-07 03:47:50
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| plink2 2.00~a5.8-231123+dfsg-1 (armhf) Sun, 07 Jan 2024 03:44:28 +0000 |
+==============================================================================+
Package: plink2
Version: 2.00~a5.8-231123+dfsg-1
Source Version: 2.00~a5.8-231123+dfsg-1
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-275ef6eb-e9d3-4a91-9add-06d93612d76f' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink2-wFkINJ/resolver-uD1B41' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.3 MB in 5s (5535 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'plink2' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/plink2.git
Please use:
git clone https://salsa.debian.org/med-team/plink2.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1174 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main plink2 2.00~a5.8-231123+dfsg-1 (dsc) [2155 B]
Get:2 http://172.17.4.1/private trixie-staging/main plink2 2.00~a5.8-231123+dfsg-1 (tar) [1119 kB]
Get:3 http://172.17.4.1/private trixie-staging/main plink2 2.00~a5.8-231123+dfsg-1 (diff) [52.3 kB]
Fetched 1174 kB in 0s (5371 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/plink2-wFkINJ/plink2-2.00~a5.8-231123+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink2-wFkINJ' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), help2man, liblapack-dev | liblapack.so, libzstd-dev, zlib1g-dev, libsimde-dev, libdeflate-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), help2man, liblapack-dev, libzstd-dev, zlib1g-dev, libsimde-dev, libdeflate-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [712 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [729 B]
Fetched 2050 B in 0s (0 B/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libblas-dev libblas3
libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libgfortran5 libicu72 liblapack-dev
liblapack3 libmagic-mgc libmagic1 libpipeline1 libsimde-dev
libsub-override-perl libtool libuchardet0 libxml2 libzstd-dev m4 man-db
po-debconf sensible-utils zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff liblapack-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libblas-dev libblas3
libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libgfortran5 libicu72 liblapack-dev
liblapack3 libmagic-mgc libmagic1 libpipeline1 libsimde-dev
libsub-override-perl libtool libuchardet0 libxml2 libzstd-dev m4 man-db
po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 42 newly installed, 0 to remove and 12 not upgraded.
Need to get 25.2 MB of archives.
After this operation, 105 MB of additional disk space will be used.
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Get:2 http://172.17.4.1/private trixie-staging/main armhf zlib1g armhf 1:1.3.dfsg-3 [74.3 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-2 [81.2 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
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Get:11 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
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Get:14 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.9 [82.3 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.9 [956 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf help2man armhf 1.49.3 [198 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libblas-dev armhf 3.11.0-2 [106 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.18-1 [45.8 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-7+rpi1 [247 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf liblapack-dev armhf 3.11.0-2 [3007 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libsimde-dev all 0.7.6-1 [384 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libzstd-dev armhf 1.5.5+dfsg2-2 [301 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12735 files and directories currently installed.)
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Setting up zlib1g:armhf (1:1.3.dfsg-3) ...
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Setting up help2man (1.49.3) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up autopoint (0.21-14) ...
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Setting up autoconf (2.71-3) ...
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Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libblas-dev:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
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 liblapack3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.21-14) ...
Setting up libtool (2.4.7-7) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up liblapack-dev:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.12.0-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-2 bsdutils_1:2.39.3-2 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-7+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.9 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 gcc-13-base_13.2.0-7+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 help2man_1.49.3 hostname_3.23+nmu1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-7+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-7+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.39.3-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-3 libcap2_1:2.66-4 libcc1-0_13.2.0-7+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.9 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.32.2-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-7+rpi1 libgcc-s1_13.2.0-7+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_13.2.0-7+rpi1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-7+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblocale-gettext-perl_1.07-6 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.3-2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-2 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-10 libpipeline1_1.5.7-1 libreadline8_8.2-3 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsimde-dev_0.7.6-1 libsmartcols1_2.39.3-2 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-glob-perl_0.11-3 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-7+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.3-2 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd-dev_1.5.5+dfsg2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20231126-1 mount_2.39.3-2 nano_7.2-1 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-10 perl-base_5.36.0-10 perl-modules-5.36_5.36.0-10 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-5 tar_1.34+dfsg-1.3 tzdata_2023c-11 usr-is-merged_38 usrmerge_38 util-linux_2.39.3-2 xz-utils_5.4.5-0.1 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: plink2
Binary: plink2
Architecture: any
Version: 2.00~a5.8-231123+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Dylan Aïssi <daissi@debian.org>
Homepage: https://www.cog-genomics.org/plink/2.0/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/plink2
Vcs-Git: https://salsa.debian.org/med-team/plink2.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), help2man, liblapack-dev | liblapack.so, libzstd-dev, zlib1g-dev, libsimde-dev, libdeflate-dev
Package-List:
plink2 deb science optional arch=any
Checksums-Sha1:
a556120f1e4b6bf09ccfea44ad3e17ec1c6106dc 1119460 plink2_2.00~a5.8-231123+dfsg.orig.tar.xz
e3d7c8b23845c466cbf0bb63cd3402cd8722b936 52288 plink2_2.00~a5.8-231123+dfsg-1.debian.tar.xz
Checksums-Sha256:
12700bff139aac4520757e6920addda8efcf84da673cd5bc1c4b800320eb222e 1119460 plink2_2.00~a5.8-231123+dfsg.orig.tar.xz
7bf66afa070435c2b44a4b22931df8f3d8ffd307c7230275c04901ec83e72721 52288 plink2_2.00~a5.8-231123+dfsg-1.debian.tar.xz
Files:
978a8223a2fd71fbc76d37f2ac4ba6e8 1119460 plink2_2.00~a5.8-231123+dfsg.orig.tar.xz
2ebf196c340bb24a3e98921457430a80 52288 plink2_2.00~a5.8-231123+dfsg-1.debian.tar.xz
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gpgv: Signature made Wed Nov 29 12:59:31 2023 UTC
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~a5.8-231123+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting plink2 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking plink2_2.00~a5.8-231123+dfsg.orig.tar.xz
dpkg-source: info: unpacking plink2_2.00~a5.8-231123+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 no_atlas.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-275ef6eb-e9d3-4a91-9add-06d93612d76f
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package plink2
dpkg-buildpackage: info: source version 2.00~a5.8-231123+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --sourcedirectory=build_dynamic/
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
cd build_dynamic && make -j4 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/build_dynamic'
rm -f plink2.1
rm -f pgen_compress.1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--sourcedirectory=build_dynamic/
dh_clean -O--sourcedirectory=build_dynamic/
debian/rules binary-arch
dh binary-arch --sourcedirectory=build_dynamic/
dh_update_autotools_config -a -O--sourcedirectory=build_dynamic/
dh_autoreconf -a -O--sourcedirectory=build_dynamic/
dh_auto_configure -a -O--sourcedirectory=build_dynamic/
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
cd build_dynamic && make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>/build_dynamic'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security ../include/SFMT.c -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../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 -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c
cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../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
../plink2.cc: In function ‘int main(int, char**)’:
../plink2.cc:5307:96: warning: ‘%s’ directive output may be truncated writing up to 2147483635 bytes into a region of size 262098 [-Wformat-truncation=]
5307 | snprintf(g_logbuf, kLogbufSize, "Error: Invalid --export vcf-dosage= argument '%s'.\n", vcf_dosage_start);
| ^~
In file included from /usr/include/stdio.h:906,
from ../include/plink2_base.h:114,
from ../include/plink2_zstfile.h:27,
from ../plink2.cc:18:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘int main(int, char**)’ at ../plink2.cc:5307:25:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: ‘__builtin___snprintf_chk’ output between 50 and 2147483685 bytes into a destination of size 262144
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/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 long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/13/bits/stl_algo.h:1854:5,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/13/bits/stl_algo.h:1942:5,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = long long unsigned int*]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
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:15198:5:
/usr/include/c++/13/bits/stl_algo.h:1859:32: warning: array subscript 16 is outside array bounds of ‘uint64_t [6]’ {aka ‘long long unsigned int [6]’} [-Warray-bounds=]
1859 | 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:15179:14: note: at offset 128 into object ‘parse_table’ of size 48
15179 | 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 -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate
/usr/bin/ld: plink2_thread.o: in function `plink2::UpdateU64IfSmaller(unsigned long long, unsigned long long*)':
./build_dynamic/../include/plink2_thread.cc:392:(.text+0x6bc): undefined reference to `__atomic_compare_exchange_8'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:182: plink2""] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build_dynamic'
dh_auto_build: error: cd build_dynamic && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make[1]: *** [debian/rules:75: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:23: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-01-07T03:47:40Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 32596
Build-Time: 162
Distribution: trixie-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 20
Job: plink2_2.00~a5.8-231123+dfsg-1
Machine Architecture: arm64
Package: plink2
Package-Time: 192
Source-Version: 2.00~a5.8-231123+dfsg-1
Space: 32596
Status: attempted
Version: 2.00~a5.8-231123+dfsg-1
--------------------------------------------------------------------------------
Finished at 2024-01-07T03:47:40Z
Build needed 00:03:12, 32596k disk space