clonalframe →
1.2-11 →
armhf → 2021-09-30 07:06:44
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| clonalframe 1.2-11 (armhf) Thu, 30 Sep 2021 06:59:21 +0000 |
+==============================================================================+
Package: clonalframe
Version: 1.2-11
Source Version: 1.2-11
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-004035e7-1c0a-403d-8d9a-f46c7c6cf0dd' 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 [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 29s (904 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: 'clonalframe' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/clonalframe.git
Please use:
git clone https://salsa.debian.org/med-team/clonalframe.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 53.5 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main clonalframe 1.2-11 (dsc) [2023 B]
Get:2 http://172.17.0.1/private bookworm-staging/main clonalframe 1.2-11 (tar) [45.5 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main clonalframe 1.2-11 (diff) [5956 B]
Fetched 53.5 kB in 0s (267 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clonalframe-4g2Ugl/clonalframe-1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalframe-4g2Ugl' 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-VITk2b/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-VITk2b/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-VITk2b/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-VITk2b/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2879 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 12 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-VITk2b/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 (22.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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), qt5-qmake, libgsl-dev
Filtered Build-Depends: debhelper-compat (= 13), qt5-qmake, libgsl-dev
dpkg-deb: building package 'sbuild-build-depends-clonalframe-dummy' in '/<<BUILDDIR>>/resolver-VITk2b/apt_archive/sbuild-build-depends-clonalframe-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-clonalframe-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-VITk2b/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ Sources [508 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ Packages [589 B]
Fetched 2430 B in 1s (3304 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install clonalframe 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 qt5-qmake qt5-qmake-bin qtchooser
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 libgsl25 libgslcblas0 libicu67
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf qt5-qmake qt5-qmake-bin qtchooser
sbuild-build-depends-clonalframe-dummy sensible-utils
0 upgraded, 38 newly installed, 0 to remove and 12 not upgraded.
Need to get 20.4 MB of archives.
After this operation, 77.5 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VITk2b/apt_archive ./ sbuild-build-depends-clonalframe-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [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 1:1.16.4-2 [819 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 1.12.0-1 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 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 qt5-qmake-bin armhf 5.15.2+dfsg-12+rpi1 [824 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf qtchooser armhf 66-2 [23.1 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf qt5-qmake armhf 5.15.2+dfsg-12+rpi1 [249 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package bsdextrautils.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.37.2-1_armhf.deb ...
Unpacking bsdextrautils (2.37.2-1) ...
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Unpacking groff-base (1.22.4-7) ...
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Unpacking sbuild-build-depends-clonalframe-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.37.2-1) ...
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 file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up qt5-qmake-bin (5.15.2+dfsg-12+rpi1) ...
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 qtchooser (66-2) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libgsl-dev (2.6+dfsg-2) ...
Setting up qt5-qmake:armhf (5.15.2+dfsg-12+rpi1) ...
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 (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.4-2) ...
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-clonalframe-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_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 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_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+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_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 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 libcc1-0_11.2.0-4+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 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+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_0.23-1 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_2.37.2-1 libmpc3_1.2.0-1 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_0.24.0-2 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_5.32.1-5 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_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+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_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+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_2.37.2-1 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_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 qt5-qmake_5.15.2+dfsg-12+rpi1 qt5-qmake-bin_5.15.2+dfsg-12+rpi1 qtchooser_66-2 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-clonalframe-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_2021a-1 util-linux_2.37.2-1 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.Ok3fMzZQ/trustedkeys.kbx': General error
gpgv: Signature made Mon Sep 27 19:36:29 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 ./clonalframe_1.2-11.dsc
dpkg-source: info: extracting clonalframe in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clonalframe_1.2.orig.tar.gz
dpkg-source: info: unpacking clonalframe_1.2-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01_gcc-4.6.patch
dpkg-source: info: applying no_qtlibs.patch
dpkg-source: info: applying glibc2.27.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-004035e7-1c0a-403d-8d9a-f46c7c6cf0dd
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clonalframe
dpkg-buildpackage: info: source version 1.2-11
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -rf bin build Makefile
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
QT_SELECT=5 CXXFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive" dh_auto_configure
qmake -makefile "QMAKE_CFLAGS_RELEASE=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now" "QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now" QMAKE_STRIP=: PREFIX=/usr
Info: creating stash file /<<PKGBUILDDIR>>/.qmake.stash
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment_xmfa.o src/alignment_xmfa.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment_structure.o src/alignment_structure.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment.o src/alignment.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/boot.o src/boot.cpp
src/alignment_structure.cpp: In constructor 'wb::Alignment_structure::Alignment_structure(char*, int)':
src/alignment_structure.cpp:45:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
45 | if (ch>='0' & ch<='9')
| ~~^~~~~
src/alignment.cpp: In member function 'void wb::Alignment::writeToFile(char*)':
src/alignment.cpp:236:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
236 | char * lets="ATCG";
| ^~~~~~
src/alignment.cpp:241:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
241 | for (unsigned int i=0;i<getB();i++) {
| ~^~~~~~~
src/alignment.cpp:243:36: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
243 | for (unsigned int j=0;j<getN();j++) {
| ~^~~~~~~
src/alignment.cpp:244:42: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
244 | for (unsigned int k=beg;k<end;k++)
| ~^~~~
src/alignment.cpp:246:38: warning: embedded '\0' in format [-Wformat-contains-nul]
246 | sprintf(buf+end-beg,"\0");
| ^~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/burst.o src/burst.cpp
src/alignment_xmfa.cpp: In constructor 'wb::Alignment_xmfa::Alignment_xmfa(char*, bool, int)':
src/alignment_xmfa.cpp:129:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
129 | for (j=0;j<strlen(bufin[i]);j++) {
| ~^~~~~~~~~~~~~~~~~
src/alignment_xmfa.cpp: In member function 'void wb::Alignment_xmfa::Fgets(char*, int, FILE*)':
src/alignment_xmfa.cpp:187:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
187 | fgets(buf,l,f);
| ~~~~~^~~~~~~~~
src/alignment_xmfa.cpp:189:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
189 | fgets(buf,l,f);
| ~~~~~^~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/consensus.o src/consensus.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/genes.o src/genes.cpp
src/genes.cpp: In constructor 'wb::Genes::Genes(wb::Alignment*, char*, char*)':
src/genes.cpp:34:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
34 | fscanf(mapf,"%d",&buf);
| ~~~~~~^~~~~~~~~~~~~~~~
src/genes.cpp:53:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
53 | fscanf(genes,"%d %d",&f1,&f2);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
src/burst.cpp: In member function 'void wb::Burst::burst(wb::Param*)':
src/burst.cpp:188:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
188 | for (k=1;k<rid->size();k++)
| ~^~~~~~~~~~~~
src/burst.cpp:190:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
190 | if (k>=rid->size()) continue;
| ~^~~~~~~~~~~~~
src/burst.cpp: In member function 'void wb::Burst::optimiseFathers(gsl_vector_int*, std::vector<std::vector<int> >*, int)':
src/burst.cpp:259:42: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
259 | if (slvs->at(prop).size()>current && !descended(prop,i,fathers)) {
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
src/burst.cpp:252:89: warning: unused parameter 'f' [-Wunused-parameter]
252 | void Burst::optimiseFathers(gsl_vector_int * fathers,vector<vector<int> > *slvs,int f) {
| ~~~~^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/hashcell.o src/hashcell.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_ages.o src/move_ages.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_delta.o src/move_delta.cpp
src/hashcell.cpp: In member function 'void wb::HashCell::addNode(wb::Tree*)':
src/hashcell.cpp:51:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
51 | if (l>=t->recMap->size) break;
| ~^~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_gap.o src/move_gap.cpp
src/move_ages.cpp: In member function 'virtual void wb::Move_ages::move(wb::Param*)':
src/move_ages.cpp:60:21: warning: suggest braces around empty body in an 'else' statement [-Wempty-body]
60 | } else ;//printf("Age change rejected because out of range\n");
| ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_hidden.o src/move_hidden.cpp
src/move_delta.cpp: In constructor 'wb::Move_delta::Move_delta(gsl_rng*, wb::Param*)':
src/move_delta.cpp:24:50: warning: unused parameter 'p' [-Wunused-parameter]
24 | Move_delta::Move_delta(gsl_rng * rng,Param * p):Move(rng) {
| ~~~~~~~~^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_hidden2.o src/move_hidden2.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_mu.o src/move_mu.cpp
src/move_gap.cpp: In constructor 'wb::Move_gap::Move_gap(gsl_rng*, wb::Param*)':
src/move_gap.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter]
24 | Move_gap::Move_gap(gsl_rng * rng,Param * p) : Move(rng) {}
| ~~~~~~~~^
src/move_hidden.cpp: In constructor 'wb::Move_hidden::Move_hidden(gsl_rng*, wb::Param*)':
src/move_hidden.cpp:25:52: warning: unused parameter 'p' [-Wunused-parameter]
25 | Move_hidden::Move_hidden(gsl_rng * rng,Param * p) : Move(rng)
| ~~~~~~~~^
src/move_hidden.cpp: In member function 'void wb::Move_hidden::forwardfast(wb::Param*, wb::Tree*)':
src/move_hidden.cpp:127:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
127 | for (unsigned int i=0;i<L;i++)
| ~^~
src/move_hidden.cpp:133:40: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
133 | for (unsigned int j=0;j<nbstates;j++) gsl_vector_set(probas,j,gsl_vector_get(pbeg,j));
| ~^~~~~~~~~
src/move_hidden.cpp:137:44: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
137 | for (unsigned int j=0;j<nbstates;j++) gsl_vector_set(probas,j,gsl_vector_get(probas,j)*gsl_matrix_get(a,j,j)*gsl_matrix_get(e,j,msgs[k]));
| ~^~~~~~~~~
src/move_hidden.cpp:132:21: warning: unused variable 'top' [-Wunused-variable]
132 | int top=0,left=0,right=0;
| ^~~
src/move_hidden.cpp:132:27: warning: unused variable 'left' [-Wunused-variable]
132 | int top=0,left=0,right=0;
| ^~~~
src/move_hidden.cpp:132:34: warning: unused variable 'right' [-Wunused-variable]
132 | int top=0,left=0,right=0;
| ^~~~~
src/move_hidden.cpp: In member function 'void wb::Move_hidden::backward(wb::Param*, gsl_matrix*, wb::Tree*)':
src/move_hidden.cpp:203:17: warning: unused variable 'd' [-Wunused-variable]
203 | int d=gsl_vector_int_get(p->a->polySites,old)- gsl_vector_int_get(p->a->polySites,old-1);
| ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_nu.o src/move_nu.cpp
src/move_mu.cpp: In constructor 'wb::Move_mu::Move_mu(gsl_rng*, wb::Param*)':
src/move_mu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter]
24 | Move_mu::Move_mu(gsl_rng * rng,Param * p):Move(rng) {}
| ~~~~~~~~^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_rho.o src/move_rho.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_wb.o src/move_wb.cpp
src/move_nu.cpp: In constructor 'wb::Move_nu::Move_nu(gsl_rng*, wb::Param*)':
src/move_nu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter]
24 | Move_nu::Move_nu(gsl_rng * rng,Param * p):Move(rng) {}
| ~~~~~~~~^
src/move_nu.cpp: In member function 'virtual void wb::Move_nu::move(wb::Param*)':
src/move_nu.cpp:56:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
56 | if (gsl_vector_char_get(t->recMap,j)==1)
| ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move.o src/move.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/param.o src/param.cpp
src/move_rho.cpp: In constructor 'wb::Move_rho::Move_rho(gsl_rng*, wb::Param*)':
src/move_rho.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter]
24 | Move_rho::Move_rho(gsl_rng * rng,Param * p):Move(rng)
| ~~~~~~~~^
src/move_wb.cpp: In member function 'virtual void wb::Move_wb::move(wb::Param*)':
src/move_wb.cpp:127:17: warning: unused variable 'sizeys2' [-Wunused-variable]
127 | int sizeys2=propLocs(ys,probys,x,p);
| ^~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/recorder.o src/recorder.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree_coal.o src/tree_coal.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree_simple.o src/tree_simple.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree_upgma.o src/tree_upgma.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree_newick.o src/tree_newick.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree.o src/tree.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/util.o src/util.cpp
src/util.cpp: In static member function 'static void wb::Util::normalize(double*, int)':
src/util.cpp:83:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
83 | for (unsigned int i=0;i<size;i++) sum+=v[i];
| ~^~~~~
src/util.cpp:85:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
85 | for (unsigned int i=0;i<size;i++) v[i]/=sum;
| ~^~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/ClonalFrame.o src/ClonalFrame.cpp
src/tree.cpp: In static member function 'static wb::Tree* wb::Tree::move(wb::Tree*, wb::Tree*, double, gsl_vector_char*, gsl_vector_char*, wb::Param*)':
src/tree.cpp:99:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
99 | if (z!=NULL)
| ^
src/tree.cpp: In member function 'double wb::Tree::llhoodb(wb::Param*)':
src/tree.cpp:229:87: warning: 'vals[9]' may be used uninitialized in this function [-Wmaybe-uninitialized]
229 | } else if (gsl_vector_char_get(recMap,i)==0) {ret+=vals[8];} else {ret+=vals[9];p->rec++;}
| ~~~^~~~~~~~~
src/tree.cpp:223:29: warning: 'vals[5]' may be used uninitialized in this function [-Wmaybe-uninitialized]
223 | {ret+=vals[5];p->rec++;}
| ~~~^~~~~~~~~
src/ClonalFrame.cpp: In function 'gsl_rng* makerng()':
src/ClonalFrame.cpp:83:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable]
83 | long int rng_seed;
| ^~~~~~~~
src/ClonalFrame.cpp: In function 'int main(int, char**)':
src/ClonalFrame.cpp:263:53: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
263 | if (cleanup==true) {a->cleanUp();a->writeToFile("/tmp/out.xmfa");}
| ^~~~~~~~~~~~~~~
src/ClonalFrame.cpp:341:42: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
341 | printf("Time spent in MH in seconds:%d\n",t2-t);
| ~^ ~~~~
| | |
| int long unsigned int
| %ld
src/ClonalFrame.cpp: In function 'gsl_rng* makerng()':
src/ClonalFrame.cpp:96:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
96 | fread(&seed,sizeof(seed),1,devrandom);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -o bin/ClonalFrame build/alignment_xmfa.o build/alignment_structure.o build/alignment.o build/boot.o build/burst.o build/consensus.o build/genes.o build/hashcell.o build/move_ages.o build/move_delta.o build/move_gap.o build/move_hidden.o build/move_hidden2.o build/move_mu.o build/move_nu.o build/move_rho.o build/move_wb.o build/move.o build/param.o build/recorder.o build/tree_coal.o build/tree_simple.o build/tree_upgma.o build/tree_newick.o build/tree.o build/util.o build/ClonalFrame.o -lgsl -lgslcblas
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install --destdir=debian/clonalframe/ -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/clonalframe/usr/bin/ClonalFrame contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'clonalframe' in '../clonalframe_1.2-11_armhf.deb'.
dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-11_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../clonalframe_1.2-11_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 2021-09-30T07:06:38Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalframe_1.2-11_armhf.changes:
---------------------------------
Format: 1.8
Date: Mon, 27 Sep 2021 21:23:54 +0200
Source: clonalframe
Binary: clonalframe clonalframe-dbgsym
Architecture: armhf
Version: 1.2-11
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clonalframe - inference of bacterial microevolution using multilocus sequence d
Changes:
clonalframe (1.2-11) unstable; urgency=medium
.
* Fix watch file
* Standards-Version: 4.6.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Remove obsolete fields Contact, Name from debian/upstream/metadata (already
present in machine-readable debian/copyright).
* watch file standard 4 (routine-update)
Checksums-Sha1:
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Checksums-Sha256:
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Files:
77d252aad66692a46ed52ef14f461ba5 247420 debug optional clonalframe-dbgsym_1.2-11_armhf.deb
626a64bbb0754a80bb49f257cf2682db 5058 science optional clonalframe_1.2-11_armhf.buildinfo
575322770602a28793375007bd7534f4 42968 science optional clonalframe_1.2-11_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalframe-dbgsym_1.2-11_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 247420 bytes: control archive=532 bytes.
384 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clonalframe-dbgsym
Source: clonalframe
Version: 1.2-11
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 273
Depends: clonalframe (= 1.2-11)
Section: debug
Priority: optional
Description: debug symbols for clonalframe
Build-Ids: 63ec225851e0204d600b8968667ae0e69c6073e9
drwxr-xr-x root/root 0 2021-09-27 19:23 ./
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/lib/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/lib/debug/.build-id/63/
-rw-r--r-- root/root 268472 2021-09-27 19:23 ./usr/lib/debug/.build-id/63/ec225851e0204d600b8968667ae0e69c6073e9.debug
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/share/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-09-27 19:23 ./usr/share/doc/clonalframe-dbgsym -> clonalframe
clonalframe_1.2-11_armhf.deb
----------------------------
new Debian package, version 2.0.
size 42968 bytes: control archive=1224 bytes.
1228 bytes, 23 lines control
577 bytes, 8 lines md5sums
Package: clonalframe
Version: 1.2-11
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 106
Depends: libc6 (>= 2.7), libgcc-s1 (>= 3.5), libgsl25 (>= 2.6), libstdc++6 (>= 5.2)
Suggests: clonalframeml
Section: science
Priority: optional
Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Description: inference of bacterial microevolution using multilocus sequence data
ClonalFrame identifies the clonal relationships between the members of
a sample, while also estimating the chromosomal position of homologous
recombination events that have disrupted the clonal inheritance.
.
ClonalFrame can be applied to any kind of sequence data, from a single
fragment of DNA to whole genomes. It is well suited for the analysis of
MLST data, where 7 gene fragments have been sequenced, but becomes
progressively more powerful as the sequenced regions increase in length
and number up to whole genomes. However, it requires the sequences to be
aligned. If you have genomic data that is not aligned, it is recommend to
use Mauve which produces alignment of whole bacterial genomes in
exactly the format required for analysis with ClonalFrame.
drwxr-xr-x root/root 0 2021-09-27 19:23 ./
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/bin/
-rwxr-xr-x root/root 87560 2021-09-27 19:23 ./usr/bin/ClonalFrame
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/share/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/share/doc/clonalframe/
-rw-r--r-- root/root 412 2021-09-27 19:23 ./usr/share/doc/clonalframe/README.Debian
-rw-r--r-- root/root 278 2021-09-27 19:23 ./usr/share/doc/clonalframe/README.test
-rw-r--r-- root/root 1360 2021-09-27 19:23 ./usr/share/doc/clonalframe/changelog.Debian.gz
-rw-r--r-- root/root 1300 2021-09-27 19:23 ./usr/share/doc/clonalframe/copyright
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/share/doc/clonalframe/examples/
-rw-r--r-- root/root 409 2021-09-27 19:23 ./usr/share/doc/clonalframe/examples/example.fasta
-rw-r--r-- root/root 344 2021-09-27 19:23 ./usr/share/doc/clonalframe/run-unit-test
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/share/man/
drwxr-xr-x root/root 0 2021-09-27 19:23 ./usr/share/man/man1/
-rw-r--r-- root/root 1055 2021-09-27 19:23 ./usr/share/man/man1/ClonalFrame.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 4464
Build-Time: 87
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 294
Job: clonalframe_1.2-11
Machine Architecture: armhf
Package: clonalframe
Package-Time: 437
Source-Version: 1.2-11
Space: 4464
Status: successful
Version: 1.2-11
--------------------------------------------------------------------------------
Finished at 2021-09-30T07:06:38Z
Build needed 00:07:17, 4464k disc space