clonalorigin →
1.0-6 →
armhf → 2021-10-27 13:31:48
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| clonalorigin 1.0-6 (armhf) Wed, 27 Oct 2021 11:15:17 +0000 |
+==============================================================================+
Package: clonalorigin
Version: 1.0-6
Source Version: 1.0-6
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-f462efc0-5b94-4e88-a096-c4ed79f547a2' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 31s (837 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 197 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main clonalorigin 1.0-6 (dsc) [1997 B]
Get:2 http://172.17.0.1/private bookworm-staging/main clonalorigin 1.0-6 (tar) [186 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main clonalorigin 1.0-6 (diff) [8736 B]
Fetched 197 kB in 0s (703 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clonalorigin-4raVmW/clonalorigin-1.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalorigin-4raVmW' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-o2Wfzf/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-o2Wfzf/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2618 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12501 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libgsl-dev, rename
Filtered Build-Depends: debhelper-compat (= 13), libgsl-dev, rename
dpkg-deb: building package 'sbuild-build-depends-clonalorigin-dummy' in '/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive/sbuild-build-depends-clonalorigin-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-clonalorigin-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ Sources [509 B]
Get:5 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ Packages [587 B]
Fetched 2429 B in 1s (3050 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install clonalorigin build dependencies (apt-based resolver)
------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
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 libgsl25 libgslcblas0 libicu67
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 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
libio-stringy-perl libpod-parser-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 libgsl25 libgslcblas0 libicu67
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf rename
sbuild-build-depends-clonalorigin-dummy sensible-utils
0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.3 MB of archives.
After this operation, 73.1 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-o2Wfzf/apt_archive ./ sbuild-build-depends-clonalorigin-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1 [823 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libgsl-dev armhf 2.6+dfsg-2 [950 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf rename all 1.13-1 [18.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package bsdextrautils.
(Reading database ... 12501 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.37.2-4_armhf.deb ...
Unpacking bsdextrautils (2.37.2-4) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ...
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Preparing to unpack .../02-groff-base_1.22.4-7_armhf.deb ...
Unpacking groff-base (1.22.4-7) ...
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Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ...
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Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
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Preparing to unpack .../05-sensible-utils_0.0.17_all.deb ...
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Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ...
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Preparing to unpack .../35-sbuild-build-depends-clonalorigin-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-clonalorigin-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libgslcblas0:armhf (2.6+dfsg-2) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libgsl25:armhf (2.6+dfsg-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up rename (1.13-1) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-2) ...
Setting up gettext (0.21-4) ...
Setting up libgsl-dev (2.6+dfsg-2) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-2) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.5-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-clonalorigin-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 gcc-10_10.3.0-11+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-9+rpi1 linux-libc-dev_5.14.9-2+rpi1
Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-11+rpi1 dash_0.5.11+git20210120+802ebd4-2 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-11+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11-base_11.2.0-9+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_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan6_11.2.0-9+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-9+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-4 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-9+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-11+rpi1 libgcc-s1_11.2.0-9+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-9+rpi1 libgpg-error0_1.42-3 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.3-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.2-2+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-9+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.5-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-9+rpi1 libuchardet0_0.0.7-1 libudev1_249.5-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.9-2+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rename_1.13-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-clonalorigin-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021d-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.pvJYN3Vb/trustedkeys.kbx': General error
gpgv: Signature made Thu Oct 21 19:09:10 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./clonalorigin_1.0-6.dsc
dpkg-source: info: extracting clonalorigin in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clonalorigin_1.0.orig.tar.gz
dpkg-source: info: unpacking clonalorigin_1.0-6.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
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-f462efc0-5b94-4e88-a096-c4ed79f547a2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clonalorigin
dpkg-buildpackage: info: source version 1.0-6
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
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'
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... /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 -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 -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 -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 -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:50:33: 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 -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 -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 -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 -Wformat -Werror=format-security -c -o warg-movedelta.o `test -f 'movedelta.cpp' || echo './'`movedelta.cpp
moveageclonal.cpp: In member function 'virtual int weakarg::MoveAgeClonal::move()':
moveageclonal.cpp:126:43: warning: 'movetemp' may be used uninitialized in this function [-Wmaybe-uninitialized]
126 | if(movetemp!=NULL) delete(movetemp);
| ^
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 -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 -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 -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 -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:157:54: warning: unused variable 'wnode' [-Wunused-variable]
157 | Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto);
| ^~~~~
moveregraftclonal.cpp:157:86: 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 -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 -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 -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 -Wformat -Werror=format-security -c -o warg-movetheta.o `test -f 'movetheta.cpp' || echo './'`movetheta.cpp
movegreedytree.cpp: In member function 'void weakarg::MoveGreedyTree::applyChanges(std::vector<double>)':
movegreedytree.cpp:230:19: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
230 | int whichto=-1,tmp;
| ^~~
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 -Wformat -Werror=format-security -c -o warg-movetimechange.o `test -f 'movetimechange.cpp' || echo './'`movetimechange.cpp
In file included from /usr/include/c++/10/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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _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 -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 -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 -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 -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 -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 -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:1112:7: 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 -Wformat -Werror=format-security -c -o warg-weakarg.o `test -f 'weakarg.cpp' || echo './'`weakarg.cpp
weakarg.cpp:40:13: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
40 | ret.append(__DATE__);
| ^~~~~~~~
weakarg.cpp:42:13: 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(weakarg::Data*&, weakarg::RecTree*&, std::vector<double>&, std::vector<int>&, std::vector<int>&, std::vector<std::__cxx11::basic_string<char> >, std::string, int)':
weakarg.cpp:342:7: warning: variable 'setregions' set but not used [-Wunused-but-set-variable]
342 | bool setregions=false;
| ^~~~~~~~~~
weakarg.cpp: In function 'bool weakarg::initializeTree(weakarg::Data*&, weakarg::RecTree*&, std::vector<std::__cxx11::basic_string<char> >, std::string)':
weakarg.cpp:404:2: 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:404:38: 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++/10/vector:72,
from node.h:4,
from tree.h:3,
from tree.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void weakarg::Tree::makeFromNewick(std::string, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from weakarg.cpp:6:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from weakarg.cpp:6:
/usr/include/c++/10/bits/stl_vector.h: In function 'weakarg::ProgramOptions& weakarg::opt()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from rectree.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void weakarg::RecTree::chooseNodePath(int, double, std::vector<int>*, std::vector<int>*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _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 -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 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'.
/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'.
/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_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_1.0-6_armhf.deb'.
dpkg-deb: building package 'clonalorigin' in '../clonalorigin_1.0-6_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../clonalorigin_1.0-6_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 2021-10-27T13:31:43Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalorigin_1.0-6_armhf.changes:
---------------------------------
Format: 1.8
Date: Thu, 21 Oct 2021 20:59:46 +0200
Source: clonalorigin
Binary: clonalorigin clonalorigin-dbgsym
Architecture: armhf
Version: 1.0-6
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clonalorigin - inference of homologous recombination in bacteria using whole gen
Closes: 984018
Changes:
clonalorigin (1.0-6) unstable; urgency=medium
.
* Fix build issue with gcc-11
Closes: #984018
* Enable uscan fetching a sensible filename
Checksums-Sha1:
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e293316ba314ea87d89273c74a89ae8a5a5e73d9 131792 clonalorigin_1.0-6_armhf.deb
Checksums-Sha256:
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Files:
3b72b2f110358f3550ad6b98c72bf08f 1587300 debug optional clonalorigin-dbgsym_1.0-6_armhf.deb
f90f741ed526391114ba609a46bb61c1 5017 science optional clonalorigin_1.0-6_armhf.buildinfo
bdeb852ba9b3980da6db4dc443af63c7 131792 science optional clonalorigin_1.0-6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalorigin-dbgsym_1.0-6_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 1587300 bytes: control archive=536 bytes.
387 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clonalorigin-dbgsym
Source: clonalorigin
Version: 1.0-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1615
Depends: clonalorigin (= 1.0-6)
Section: debug
Priority: optional
Description: debug symbols for clonalorigin
Build-Ids: 9ecb365d74458dde709f3000bfe608e21bc1bad4
drwxr-xr-x root/root 0 2021-10-21 18:59 ./
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/lib/debug/.build-id/9e/
-rw-r--r-- root/root 1642952 2021-10-21 18:59 ./usr/lib/debug/.build-id/9e/cb365d74458dde709f3000bfe608e21bc1bad4.debug
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/share/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-21 18:59 ./usr/share/doc/clonalorigin-dbgsym -> clonalorigin
clonalorigin_1.0-6_armhf.deb
----------------------------
new Debian package, version 2.0.
size 131792 bytes: control archive=1164 bytes.
1072 bytes, 20 lines control
507 bytes, 8 lines md5sums
Package: clonalorigin
Version: 1.0-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 341
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgsl25 (>= 2.6), libstdc++6 (>= 5.2)
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 2021-10-21 18:59 ./
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/bin/
-rwxr-xr-x root/root 430 2021-10-21 18:59 ./usr/bin/blocksplit
lrwxrwxrwx root/root 0 2021-10-21 18:59 ./usr/bin/clonalorigin -> warg
-rwxr-xr-x root/root 3039 2021-10-21 18:59 ./usr/bin/computeMedians
-rwxr-xr-x root/root 1111 2021-10-21 18:59 ./usr/bin/makeMauveWargFile
-rwxr-xr-x root/root 326272 2021-10-21 18:59 ./usr/bin/warg
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/share/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/share/doc/clonalorigin/
-rw-r--r-- root/root 504 2021-10-21 18:59 ./usr/share/doc/clonalorigin/README.Debian
-rw-r--r-- root/root 639 2021-10-21 18:59 ./usr/share/doc/clonalorigin/changelog.Debian.gz
-rw-r--r-- root/root 542 2021-10-21 18:59 ./usr/share/doc/clonalorigin/copyright
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-21 18:59 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2021-10-21 18:59 ./usr/share/man/man1/clonalorigin.1.gz -> warg.1.gz
-rw-r--r-- root/root 1604 2021-10-21 18:59 ./usr/share/man/man1/warg.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 27424
Build-Time: 7806
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 324
Job: clonalorigin_1.0-6
Machine Architecture: armhf
Package: clonalorigin
Package-Time: 8186
Source-Version: 1.0-6
Space: 27424
Status: successful
Version: 1.0-6
--------------------------------------------------------------------------------
Finished at 2021-10-27T13:31:43Z
Build needed 02:16:26, 27424k disc space