clonalorigin →
1.0-8 →
armhf → 2023-12-31 05:12:15
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| clonalorigin 1.0-8 (armhf) Sun, 31 Dec 2023 05:09:34 +0000 |
+==============================================================================+
Package: clonalorigin
Version: 1.0-8
Source Version: 1.0-8
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-5fe6698b-17f9-45fc-b960-998827bc7cb2' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/clonalorigin-Umsc4W/resolver-fgLrxq' 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 (5558 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: 'clonalorigin' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/clonalorigin.git
Please use:
git clone https://salsa.debian.org/med-team/clonalorigin.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 199 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main clonalorigin 1.0-8 (dsc) [2183 B]
Get:2 http://172.17.4.1/private trixie-staging/main clonalorigin 1.0-8 (tar) [186 kB]
Get:3 http://172.17.4.1/private trixie-staging/main clonalorigin 1.0-8 (diff) [10.6 kB]
Fetched 199 kB in 0s (2096 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clonalorigin-Umsc4W/clonalorigin-1.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalorigin-Umsc4W' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libgsl-dev, rename, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libgsl-dev, rename, 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 [637 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [669 B]
Fetched 1915 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 intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libgsl-dev libgsl27 libgslcblas0 libicu72
libmagic-mgc libmagic1 libpipeline1 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf rename sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html 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 intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libgsl-dev libgsl27 libgslcblas0 libicu72
libmagic-mgc libmagic1 libpipeline1 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf rename
sbuild-build-depends-main-dummy sensible-utils
0 upgraded, 35 newly installed, 0 to remove and 11 not upgraded.
Need to get 20.0 MB of archives.
After this operation, 78.7 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-2 [81.2 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.9 [82.3 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.9 [956 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libgslcblas0 armhf 2.7.1+dfsg-6 [79.3 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libgsl27 armhf 2.7.1+dfsg-6 [753 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libgsl-dev armhf 2.7.1+dfsg-6 [965 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf rename all 2.01-2 [21.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 20.0 MB in 2s (8589 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12735 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.8-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.8-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../01-groff-base_1.23.0-3_armhf.deb ...
Unpacking groff-base (1.23.0-3) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../02-bsdextrautils_2.39.3-2_armhf.deb ...
Unpacking bsdextrautils (2.39.3-2) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.7-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.12.0-1_armhf.deb ...
Unpacking man-db (2.12.0-1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../05-sensible-utils_0.0.20_all.deb ...
Unpacking sensible-utils (0.0.20) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../06-libmagic-mgc_1%3a5.45-2_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../07-libmagic1_1%3a5.45-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.45-2) ...
Selecting previously unselected package file.
Preparing to unpack .../08-file_1%3a5.45-2_armhf.deb ...
Unpacking file (1:5.45-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../09-gettext-base_0.21-14_armhf.deb ...
Unpacking gettext-base (0.21-14) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-14_all.deb ...
Unpacking autopoint (0.21-14) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.11.9_all.deb ...
Unpacking libdebhelper-perl (13.11.9) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-7_all.deb ...
Unpacking libtool (2.4.7-7) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ...
Unpacking libsub-override-perl (0.10-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../22-libelf1_0.188-2.1+rpi1_armhf.deb ...
Unpacking libelf1:armhf (0.188-2.1+rpi1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1_armhf.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../24-libicu72_72.1-4_armhf.deb ...
Unpacking libicu72:armhf (72.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3_armhf.deb ...
Unpacking libxml2:armhf (2.9.14+dfsg-1.3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-14_armhf.deb ...
Unpacking gettext (0.21-14) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.11.9_all.deb ...
Unpacking debhelper (13.11.9) ...
Selecting previously unselected package libgslcblas0:armhf.
Preparing to unpack .../30-libgslcblas0_2.7.1+dfsg-6_armhf.deb ...
Unpacking libgslcblas0:armhf (2.7.1+dfsg-6) ...
Selecting previously unselected package libgsl27:armhf.
Preparing to unpack .../31-libgsl27_2.7.1+dfsg-6_armhf.deb ...
Unpacking libgsl27:armhf (2.7.1+dfsg-6) ...
Selecting previously unselected package libgsl-dev.
Preparing to unpack .../32-libgsl-dev_2.7.1+dfsg-6_armhf.deb ...
Unpacking libgsl-dev (2.7.1+dfsg-6) ...
Selecting previously unselected package rename.
Preparing to unpack .../33-rename_2.01-2_all.deb ...
Unpacking rename (2.01-2) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../34-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.3-2) ...
Setting up libgslcblas0:armhf (2.7.1+dfsg-6) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.9) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up gettext-base (0.21-14) ...
Setting up libgsl27:armhf (2.7.1+dfsg-6) ...
Setting up m4 (1.4.19-4) ...
Setting up rename (2.01-2) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up file (1:5.45-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-14) ...
Setting up autoconf (2.71-3) ...
Setting up sensible-utils (0.0.20) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
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 (0.21-14) ...
Setting up libgsl-dev (2.7.1+dfsg-6) ...
Setting up libtool (2.4.7-7) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
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'.
Setting up debhelper (13.11.9) ...
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 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 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 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 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-7+rpi1 libgpg-error0_1.47-3 libgsl-dev_2.7.1+dfsg-6 libgsl27_2.7.1+dfsg-6 libgslcblas0_2.7.1+dfsg-6 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 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 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 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 rename_2.01-2 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_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: clonalorigin
Binary: clonalorigin
Architecture: any
Version: 1.0-8
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/xavierdidelot/clonalorigin
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/clonalorigin
Vcs-Git: https://salsa.debian.org/med-team/clonalorigin.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libgsl-dev, rename
Package-List:
clonalorigin deb science optional arch=any
Checksums-Sha1:
a7bc183ea6aea575a5f5fa9217d9112d2ff4884f 185865 clonalorigin_1.0.orig.tar.gz
8b84785b3d7ffb55e62b2b9932c4c62ec9900f03 10608 clonalorigin_1.0-8.debian.tar.xz
Checksums-Sha256:
73962415160b8b496c81d3e9cbbf68f76c02caf4dd6b41860f01d493b71c6e3a 185865 clonalorigin_1.0.orig.tar.gz
192e0da0642eea3f9e86d40b535ac89c900be9cfe557d163ca29a54e7f479882 10608 clonalorigin_1.0-8.debian.tar.xz
Files:
310a0c5714e7629c052ab4da50c90f44 185865 clonalorigin_1.0.orig.tar.gz
905b8b38da217ad00e12e9f849ec267d 10608 clonalorigin_1.0-8.debian.tar.xz
Dgit: b3fc1b67fb518bb450b668e97a3abd1aad93e880 debian archive/debian/1.0-8 https://git.dgit.debian.org/clonalorigin
-----BEGIN PGP SIGNATURE-----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=dgh7
-----END PGP SIGNATURE-----
gpgv: Signature made Fri Dec 29 12:20:18 2023 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./clonalorigin_1.0-8.dsc: no acceptable signature found
dpkg-source: info: extracting clonalorigin in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clonalorigin_1.0.orig.tar.gz
dpkg-source: info: unpacking clonalorigin_1.0-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying portability.patch
dpkg-source: info: applying gcc-11.patch
dpkg-source: info: applying shorten-test.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-5fe6698b-17f9-45fc-b960-998827bc7cb2
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 clonalorigin
dpkg-buildpackage: info: source version 1.0-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --sourcedirectory=warg
dh_auto_clean -O--sourcedirectory=warg
debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
test ! -e warg/src/truth.xml.preserve \
|| mv -v warg/src/truth.xml.preserve warg/src/truth.xml
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--sourcedirectory=warg
dh_clean -O--sourcedirectory=warg
debian/rules binary-arch
dh binary-arch --sourcedirectory=warg
dh_update_autotools_config -a -O--sourcedirectory=warg
dh_autoreconf -a -O--sourcedirectory=warg
configure.ac:58: warning: The macro `AC_TRY_RUN' is obsolete.
configure.ac:58: You should run autoupdate.
./lib/autoconf/general.m4:2997: AC_TRY_RUN is expanded from...
m4/gsl.m4:5: AX_PATH_GSL is expanded from...
configure.ac:58: the top level
configure.ac:58: warning: The macro `AC_TRY_LINK' is obsolete.
configure.ac:58: You should run autoupdate.
./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from...
m4/gsl.m4:5: AX_PATH_GSL is expanded from...
configure.ac:58: the top level
configure.ac:41: installing 'config/compile'
configure.ac:9: installing 'config/install-sh'
configure.ac:9: installing 'config/missing'
Makefile.am: installing './INSTALL'
src/Makefile.am: installing 'config/depcomp'
parallel-tests: installing 'config/test-driver'
debian/rules execute_before_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp -v warg/src/truth.xml warg/src/truth.xml.preserve
'warg/src/truth.xml' -> 'warg/src/truth.xml.preserve'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_configure -a -O--sourcedirectory=warg
cd warg && ./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
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/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 the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 0.2.5... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for inline... inline
checking for floor... no
checking for pow... no
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 scripts/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
dh_auto_build -a -O--sourcedirectory=warg
cd warg && make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>/warg'
Making all in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make all-am
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-data.o `test -f 'data.cpp' || echo './'`data.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-rng.o `test -f 'rng.cpp' || echo './'`rng.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-wargxml.o `test -f 'wargxml.cpp' || echo './'`wargxml.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-move.o `test -f 'move.cpp' || echo './'`move.cpp
data.cpp: In constructor ‘weakarg::Data::Data(std::string)’:
data.cpp:50:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
50 | }else if(getNumber(tmpname)!=which){
| ~~~~~~~~~~~~~~~~~~^~~~~~~
data.cpp: In member function ‘void weakarg::Data::subset(std::vector<int>, int)’:
data.cpp:169:14: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
169 | if (num<=0 &&seed>=0 || num<0) return;
| ~~~~~~~^~~~~~~~~
data.cpp:177:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
177 | for(int i=0;i<numv.size();i++) if(numv[i]<tried.size()&&numv[i]>=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<<numv[i]<<" were specified and have been removed from the analysis."<<endl;}}else{cerr<<"Warning: Invalid blocks were specified and have been removed from the analysis."<<endl;}
| ~^~~~~~~~~~~~
data.cpp:177:46: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} and ‘std::vector<bool>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
177 | for(int i=0;i<numv.size();i++) if(numv[i]<tried.size()&&numv[i]>=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<<numv[i]<<" were specified and have been removed from the analysis."<<endl;}}else{cerr<<"Warning: Invalid blocks were specified and have been removed from the analysis."<<endl;}
rng.cpp: In function ‘long unsigned int weakarg::makerng(bool)’:
rng.cpp:17:14: warning: variable ‘rng_seed’ set but not used [-Wunused-but-set-variable]
17 | long int rng_seed;
| ^~~~~~~~
rng.cpp: In function ‘int weakarg::loadrng(std::string)’:
rng.cpp:67:14: warning: variable ‘rng_seed’ set but not used [-Wunused-but-set-variable]
67 | long int rng_seed;
| ^~~~~~~~
rng.cpp: In function ‘long unsigned int weakarg::seedrng(long unsigned int)’:
rng.cpp:41:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
41 | fread(&tseed,sizeof(tseed),1,devrandom);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-metropolis.o `test -f 'metropolis.cpp' || echo './'`metropolis.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-moveaddedge.o `test -f 'moveaddedge.cpp' || echo './'`moveaddedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-moveageclonal.o `test -f 'moveageclonal.cpp' || echo './'`moveageclonal.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-movedelta.o `test -f 'movedelta.cpp' || echo './'`movedelta.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-moveedgechange.o `test -f 'moveedgechange.cpp' || echo './'`moveedgechange.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-moveregraftclonal.o `test -f 'moveregraftclonal.cpp' || echo './'`moveregraftclonal.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-moveremedge.o `test -f 'moveremedge.cpp' || echo './'`moveremedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-moverho.o `test -f 'moverho.cpp' || echo './'`moverho.cpp
moveregraftclonal.cpp: In member function ‘virtual int weakarg::MoveRegraftClonal::move()’:
moveregraftclonal.cpp:43:9: warning: unused variable ‘notmovednode’ [-Wunused-variable]
43 | int notmovednode=rectree->otherChild(origfather,which);
| ^~~~~~~~~~~~
moveregraftclonal.cpp: In member function ‘void weakarg::MoveRegraftClonal::regraft(int, int)’:
moveregraftclonal.cpp:157:61: warning: unused variable ‘wnode’ [-Wunused-variable]
157 | Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto);
| ^~~~~
moveregraftclonal.cpp:157:93: warning: unused variable ‘wtonode’ [-Wunused-variable]
157 | Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto);
| ^~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-movescaletree.o `test -f 'movescaletree.cpp' || echo './'`movescaletree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-movegreedytree.o `test -f 'movegreedytree.cpp' || echo './'`movegreedytree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-movesitechange.o `test -f 'movesitechange.cpp' || echo './'`movesitechange.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-movetheta.o `test -f 'movetheta.cpp' || echo './'`movetheta.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-movetimechange.o `test -f 'movetimechange.cpp' || echo './'`movetimechange.cpp
movegreedytree.cpp: In member function ‘void weakarg::MoveGreedyTree::applyChanges(std::vector<double>)’:
movegreedytree.cpp:230:26: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
230 | int whichto=-1,tmp;
| ^~~
In file included from /usr/include/c++/13/vector:72,
from data.h:3,
from param.h:3,
from move.h:4,
from movesitechange.h:4,
from movesitechange.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)’ at movesitechange.cpp:139:19:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)’ at movesitechange.cpp:145:30:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)’ at movesitechange.cpp:149:30:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)’ at movesitechange.cpp:154:30:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)’ at movesitechange.cpp:158:30:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)’ at movesitechange.cpp:162:23:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-mpiutils.o `test -f 'mpiutils.cpp' || echo './'`mpiutils.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-node.o `test -f 'node.cpp' || echo './'`node.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-param.o `test -f 'param.cpp' || echo './'`param.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-recedge.o `test -f 'recedge.cpp' || echo './'`recedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-rectree.o `test -f 'rectree.cpp' || echo './'`rectree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-tree.o `test -f 'tree.cpp' || echo './'`tree.cpp
rectree.cpp: In member function ‘int weakarg::RecTree::moveNodeTime(int, int*, double, int, std::vector<int>*, std::vector<int>*)’:
rectree.cpp:1112:14: warning: variable ‘newfather’ set but not used [-Wunused-but-set-variable]
1112 | int newfather,notnewfather;
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o warg-weakarg.o `test -f 'weakarg.cpp' || echo './'`weakarg.cpp
weakarg.cpp:40:20: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
40 | ret.append(__DATE__);
| ^~~~~~~~
weakarg.cpp:42:20: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
42 | ret.append(__TIME__);
| ^~~~~~~~
weakarg.cpp: In function ‘int main(int, char**)’:
weakarg.cpp:127:10: warning: variable ‘setregions’ set but not used [-Wunused-but-set-variable]
127 | bool setregions=false;
| ^~~~~~~~~~
weakarg.cpp: In function ‘std::vector<double> weakarg::readInputFiles(Data*&, RecTree*&, std::vector<double>&, std::vector<int>&, std::vector<int>&, std::vector<std::__cxx11::basic_string<char> >, std::string, int)’:
weakarg.cpp:342:14: warning: variable ‘setregions’ set but not used [-Wunused-but-set-variable]
342 | bool setregions=false;
| ^~~~~~~~~~
weakarg.cpp: In function ‘bool weakarg::initializeTree(Data*&, RecTree*&, std::vector<std::__cxx11::basic_string<char> >, std::string)’:
weakarg.cpp:404:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
404 | if(readparams) p->setTheta(pars[2]);p->setRho(pars[0]);p->setDelta(pars[2]);
| ^~
weakarg.cpp:404:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
404 | if(readparams) p->setTheta(pars[2]);p->setRho(pars[0]);p->setDelta(pars[2]);
| ^
In file included from /usr/include/c++/13/vector:72,
from node.h:4,
from tree.h:3,
from tree.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void weakarg::Tree::makeFromNewick(std::string, bool)’ at tree.cpp:60:28:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void weakarg::Tree::makeFromNewick(std::string, bool)’ at tree.cpp:62:28:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void weakarg::Tree::makeFromNewick(std::string, bool)’ at tree.cpp:72:23:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from weakarg.cpp:6:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘weakarg::ProgramOptions::ProgramOptions()’ at weakarg.h:40:16,
inlined from ‘weakarg::ProgramOptions& weakarg::opt()’ at weakarg.cpp:25:24:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from rectree.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void weakarg::RecTree::chooseNodePath(int, double, std::vector<int>*, std::vector<int>*)’ at rectree.cpp:1064:53:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wl,-z,relro -Wl,-z,now -o warg warg-data.o warg-rng.o warg-wargxml.o warg-move.o warg-metropolis.o warg-moveaddedge.o warg-moveageclonal.o warg-movedelta.o warg-moveedgechange.o warg-moveregraftclonal.o warg-moveremedge.o warg-moverho.o warg-movescaletree.o warg-movegreedytree.o warg-movesitechange.o warg-movetheta.o warg-movetimechange.o warg-mpiutils.o warg-node.o warg-param.o warg-recedge.o warg-rectree.o warg-tree.o warg-weakarg.o -L/usr/lib/arm-linux-gnueabihf -lgsl -lgslcblas -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
Making all in scripts
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/warg'
dh_auto_test -a -O--sourcedirectory=warg
cd warg && make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/warg'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make profilerun.sh
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make[3]: 'profilerun.sh' is up to date.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make check-TESTS
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
PASS: profilerun.sh
============================================================================
Testsuite summary for clonalorigin 0.0.1
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
Making check in scripts
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/warg'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--sourcedirectory=warg
dh_prep -a -O--sourcedirectory=warg
dh_auto_install --destdir=debian/clonalorigin/ -a -O--sourcedirectory=warg
cd warg && make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/clonalorigin AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>/warg'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/clonalorigin/usr/bin'
/usr/bin/install -c warg '/<<PKGBUILDDIR>>/debian/clonalorigin/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
Making install in scripts
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/clonalorigin/usr/bin'
/usr/bin/install -c blocksplit.pl computeMedians.pl makeMauveWargFile.pl '/<<PKGBUILDDIR>>/debian/clonalorigin/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg'
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg'
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>>/warg'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/warg'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
rename 's/\.pl//' debian/clonalorigin/usr/bin/*.pl
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a -O--sourcedirectory=warg
dh_installchangelogs -a -O--sourcedirectory=warg
dh_installman -a -O--sourcedirectory=warg
dh_installsystemduser -a -O--sourcedirectory=warg
dh_lintian -a -O--sourcedirectory=warg
dh_perl -a -O--sourcedirectory=warg
dh_link -a -O--sourcedirectory=warg
dh_strip_nondeterminism -a -O--sourcedirectory=warg
dh_compress -a -O--sourcedirectory=warg
dh_fixperms -a -O--sourcedirectory=warg
dh_missing -a -O--sourcedirectory=warg
dh_dwz -a -O--sourcedirectory=warg
dh_strip -a -O--sourcedirectory=warg
dh_makeshlibs -a -O--sourcedirectory=warg
dh_shlibdeps -a -O--sourcedirectory=warg
dpkg-shlibdeps: warning: debian/clonalorigin/usr/bin/warg 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/clonalorigin/usr/bin/warg was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a -O--sourcedirectory=warg
dh_gencontrol -a -O--sourcedirectory=warg
dpkg-gencontrol: warning: package clonalorigin: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package clonalorigin: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a -O--sourcedirectory=warg
dh_builddeb -a -O--sourcedirectory=warg
dpkg-deb: building package 'clonalorigin-dbgsym' in '../clonalorigin-dbgsym_1.0-8_armhf.deb'.
dpkg-deb: building package 'clonalorigin' in '../clonalorigin_1.0-8_armhf.deb'.
dpkg-genbuildinfo --build=any -O../clonalorigin_1.0-8_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../clonalorigin_1.0-8_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 2023-12-31T05:12:11Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalorigin_1.0-8_armhf.changes:
---------------------------------
Format: 1.8
Date: Fri, 29 Dec 2023 13:11:47 +0100
Source: clonalorigin
Binary: clonalorigin clonalorigin-dbgsym
Architecture: armhf
Version: 1.0-8
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
clonalorigin - inference of homologous recombination in bacteria using whole gen
Closes: 884475
Changes:
clonalorigin (1.0-8) unstable; urgency=medium
.
* shorten-test.patch: new: reduce stress on buildds. (Closes: #884475)
* d/tests/: new: add autopkgtest.
* clonalorigin-gui.1: minor fixups.
* d/blocksplit.1: new: document upstream script.
* d/computeMedians.1: new: document upstream script.
* d/makeMauveWargFile.1: new: document upstream script.
* d/clonalorigin-gui.1: minor fixup.
* d/warg.1: minor fixup in description.
* d/clonalorigin.1: remove: unused.
The real manual page in the binary package is a link to warg(1).
* d/clonalorigin.manpages: add missing script manuals.
* d/control: recommend libxml-parser-perl.
This library is needed by computeMedians, although it does not seem
critical to typical clonalorigin workloads.
* d/*lintian-overrides: new: flag a false positive.
Checksums-Sha1:
e3cbd6b8aeb14d25ee9fecb35ac908430130f91d 1642792 clonalorigin-dbgsym_1.0-8_armhf.deb
298d23c5b8b13fd7fd7eb8d34a77b21dea3bbde5 5369 clonalorigin_1.0-8_armhf.buildinfo
942428c5ec837da90f999cd7c34a7f988b2426ae 140540 clonalorigin_1.0-8_armhf.deb
Checksums-Sha256:
d9700e111873eb037c69513c4aa22acfca567967ca9cbe20a0241517ef35056e 1642792 clonalorigin-dbgsym_1.0-8_armhf.deb
a0a00fcba75e33d544e047048560bc3dd5ad8fc8765dc4afd7d988ab3394e6ed 5369 clonalorigin_1.0-8_armhf.buildinfo
f2e22b44a9c3e4f27f920e29e5f41fc56626041aefd46f1a14765f5d480d4eaa 140540 clonalorigin_1.0-8_armhf.deb
Files:
52b33ea711228fb8cea25247ab609fb8 1642792 debug optional clonalorigin-dbgsym_1.0-8_armhf.deb
1f82833c36c13725a6ea61edfc4378f1 5369 science optional clonalorigin_1.0-8_armhf.buildinfo
3a04c409c9060e8af5dd76c2473339e8 140540 science optional clonalorigin_1.0-8_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: clonalorigin
Binary: clonalorigin clonalorigin-dbgsym
Architecture: armhf
Version: 1.0-8
Checksums-Md5:
52b33ea711228fb8cea25247ab609fb8 1642792 clonalorigin-dbgsym_1.0-8_armhf.deb
3a04c409c9060e8af5dd76c2473339e8 140540 clonalorigin_1.0-8_armhf.deb
Checksums-Sha1:
e3cbd6b8aeb14d25ee9fecb35ac908430130f91d 1642792 clonalorigin-dbgsym_1.0-8_armhf.deb
942428c5ec837da90f999cd7c34a7f988b2426ae 140540 clonalorigin_1.0-8_armhf.deb
Checksums-Sha256:
d9700e111873eb037c69513c4aa22acfca567967ca9cbe20a0241517ef35056e 1642792 clonalorigin-dbgsym_1.0-8_armhf.deb
f2e22b44a9c3e4f27f920e29e5f41fc56626041aefd46f1a14765f5d480d4eaa 140540 clonalorigin_1.0-8_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sun, 31 Dec 2023 05:12:11 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
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),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-7+rpi1),
gcc (= 4:13.2.0-1+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),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-7+rpi1),
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),
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),
libdpkg-perl (= 1.22.1+rpi1),
libelf1 (= 0.188-2.1+rpi1),
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),
libgmp10 (= 2:6.3.0+dfsg-2),
libgomp1 (= 13.2.0-7+rpi1),
libgpg-error0 (= 1.47-3),
libgsl-dev (= 2.7.1+dfsg-6),
libgsl27 (= 2.7.1+dfsg-6),
libgslcblas0 (= 2.7.1+dfsg-6),
libgssapi-krb5-2 (= 1.20.1-5),
libicu72 (= 72.1-4),
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),
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),
libnsl-dev (= 1.3.0-3),
libnsl2 (= 1.3.0-3),
libnumber-compare-perl (= 0.03-3),
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),
libseccomp2 (= 2.5.4-2+rpi1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.3-2),
libssl3 (= 3.1.4-2),
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),
libtext-glob-perl (= 0.11-3),
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),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-1),
mawk (= 1.3.4.20231126-1),
ncurses-base (= 6.4+20231209-1),
ncurses-bin (= 6.4+20231209-1),
patch (= 2.7.6-7),
perl (= 5.36.0-10),
perl-base (= 5.36.0-10),
perl-modules-5.36 (= 5.36.0-10),
po-debconf (= 1.0.21+nmu1),
rename (= 2.01-2),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-5),
tar (= 1.34+dfsg-1.3),
usr-is-merged (= 38),
usrmerge (= 38),
util-linux (= 2.39.3-2),
xz-utils (= 5.4.5-0.1),
zlib1g (= 1:1.2.13.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1703851907"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalorigin-dbgsym_1.0-8_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 1642792 bytes: control archive=536 bytes.
387 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clonalorigin-dbgsym
Source: clonalorigin
Version: 1.0-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1658
Depends: clonalorigin (= 1.0-8)
Section: debug
Priority: optional
Description: debug symbols for clonalorigin
Build-Ids: 58d86c29a702a9ed822669cc46e1b2bd7937c823
drwxr-xr-x root/root 0 2023-12-29 12:11 ./
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/lib/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/lib/debug/.build-id/58/
-rw-r--r-- root/root 1687492 2023-12-29 12:11 ./usr/lib/debug/.build-id/58/d86c29a702a9ed822669cc46e1b2bd7937c823.debug
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-12-29 12:11 ./usr/share/doc/clonalorigin-dbgsym -> clonalorigin
clonalorigin_1.0-8_armhf.deb
----------------------------
new Debian package, version 2.0.
size 140540 bytes: control archive=1300 bytes.
1107 bytes, 21 lines control
800 bytes, 12 lines md5sums
Package: clonalorigin
Version: 1.0-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 364
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libstdc++6 (>= 13.1)
Recommends: libxml-parserl-perl
Section: science
Priority: optional
Homepage: https://github.com/xavierdidelot/clonalorigin
Description: inference of homologous recombination in bacteria using whole genome sequences
Bacteria, unlike us, can reproduce on their own. They do however have
mechanisms that transfer DNA between organisms, a process more formally
known as recombination. The mechanisms by which recombination takes
place have been studied extensively in the laboratory but much remains
to be understood concerning how, when and where recombination takes
place within natural populations of bacteria and how it helps them to
adapt to new environments. ClonalOrigin performs a comparative analysis
of the sequences of a sample of bacterial genomes in order to
reconstruct the recombination events that have taken place in their
ancestry.
drwxr-xr-x root/root 0 2023-12-29 12:11 ./
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/bin/
-rwxr-xr-x root/root 430 2023-12-29 12:11 ./usr/bin/blocksplit
lrwxrwxrwx root/root 0 2023-12-29 12:11 ./usr/bin/clonalorigin -> warg
-rwxr-xr-x root/root 3039 2023-12-29 12:11 ./usr/bin/computeMedians
-rwxr-xr-x root/root 1111 2023-12-29 12:11 ./usr/bin/makeMauveWargFile
-rwxr-xr-x root/root 342656 2023-12-29 12:11 ./usr/bin/warg
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/doc/clonalorigin/
-rw-r--r-- root/root 504 2023-12-29 12:11 ./usr/share/doc/clonalorigin/README.Debian
-rw-r--r-- root/root 1061 2023-12-29 12:11 ./usr/share/doc/clonalorigin/changelog.Debian.gz
-rw-r--r-- root/root 542 2023-12-29 12:11 ./usr/share/doc/clonalorigin/copyright
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/lintian/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 124 2023-12-29 12:11 ./usr/share/lintian/overrides/clonalorigin
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/man/
drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/man/man1/
-rw-r--r-- root/root 529 2023-12-29 12:11 ./usr/share/man/man1/blocksplit.1.gz
lrwxrwxrwx root/root 0 2023-12-29 12:11 ./usr/share/man/man1/clonalorigin.1.gz -> warg.1.gz
-rw-r--r-- root/root 423 2023-12-29 12:11 ./usr/share/man/man1/computeMedians.1.gz
-rw-r--r-- root/root 421 2023-12-29 12:11 ./usr/share/man/man1/makeMauveWargFile.1.gz
-rw-r--r-- root/root 1602 2023-12-29 12:11 ./usr/share/man/man1/warg.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 24640
Build-Time: 133
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 15
Job: clonalorigin_1.0-8
Machine Architecture: arm64
Package: clonalorigin
Package-Time: 157
Source-Version: 1.0-8
Space: 24640
Status: successful
Version: 1.0-8
--------------------------------------------------------------------------------
Finished at 2023-12-31T05:12:11Z
Build needed 00:02:37, 24640k disk space