clonalframe →
1.2-11+b2 →
armhf → 2024-08-05 19:10:42
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| clonalframe 1.2-11+b2 (armhf) Mon, 05 Aug 2024 18:31:11 +0000 |
+==============================================================================+
Package: clonalframe
Version: 1.2-11+b2
Source Version: 1.2-11
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-98bfe556-22ff-4e9f-a367-b805017e7a33' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/clonalframe-aUmBTo/resolver-vxdwX4' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.6 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.1 MB]
Fetched 29.7 MB in 5s (5592 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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://172.17.4.1/private trixie-staging/main clonalframe 1.2-11 (dsc) [2023 B]
Get:2 http://172.17.4.1/private trixie-staging/main clonalframe 1.2-11 (tar) [45.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main clonalframe 1.2-11 (diff) [5956 B]
Fetched 53.5 kB in 0s (750 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clonalframe-aUmBTo/clonalframe-1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalframe-aUmBTo' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), qt5-qmake, libgsl-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), qt5-qmake, libgsl-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [640 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [672 B]
Fetched 1921 B in 0s (0 B/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates cron cron-daemon-common dbus dbus-bin dbus-daemon
dbus-session-bus-common dbus-system-bus-common dmsetup
libalgorithm-diff-perl libalgorithm-merge-perl libapparmor1
libarchive-cpio-perl libcryptsetup12 libdbus-1-3 libdevmapper1.02.1
libexpat1 libfdisk1 libfile-fcntllock-perl libjson-c5 libkmod2 libltdl-dev
libltdl7 libmail-sendmail-perl libsys-hostname-long-perl libsystemd-shared
netbase openssl systemd systemd-dev systemd-timesyncd
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
libgsl-dev libgsl28 libgslcblas0 qt5-qmake qt5-qmake-bin qtchooser
Suggested packages:
gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html
The following NEW packages will be installed:
libgsl-dev libgsl28 libgslcblas0 qt5-qmake qt5-qmake-bin qtchooser
sbuild-build-depends-main-dummy
0 upgraded, 7 newly installed, 0 to remove and 44 not upgraded.
Need to get 2944 kB of archives.
After this operation, 13.2 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libgslcblas0 armhf 2.8+dfsg-3 [79.0 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libgsl28 armhf 2.8+dfsg-3 [795 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf libgsl-dev armhf 2.8+dfsg-3 [1009 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf qt5-qmake-bin armhf 5.15.13+dfsg-4+rpi1 [813 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf qtchooser armhf 66-2 [23.1 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf qt5-qmake armhf 5.15.13+dfsg-4+rpi1 [223 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2944 kB in 0s (7291 kB/s)
Selecting previously unselected package libgslcblas0:armhf.
(Reading database ... 16263 files and directories currently installed.)
Preparing to unpack .../0-libgslcblas0_2.8+dfsg-3_armhf.deb ...
Unpacking libgslcblas0:armhf (2.8+dfsg-3) ...
Selecting previously unselected package libgsl28:armhf.
Preparing to unpack .../1-libgsl28_2.8+dfsg-3_armhf.deb ...
Unpacking libgsl28:armhf (2.8+dfsg-3) ...
Selecting previously unselected package libgsl-dev.
Preparing to unpack .../2-libgsl-dev_2.8+dfsg-3_armhf.deb ...
Unpacking libgsl-dev (2.8+dfsg-3) ...
Selecting previously unselected package qt5-qmake-bin.
Preparing to unpack .../3-qt5-qmake-bin_5.15.13+dfsg-4+rpi1_armhf.deb ...
Unpacking qt5-qmake-bin (5.15.13+dfsg-4+rpi1) ...
Selecting previously unselected package qtchooser.
Preparing to unpack .../4-qtchooser_66-2_armhf.deb ...
Unpacking qtchooser (66-2) ...
Selecting previously unselected package qt5-qmake:armhf.
Preparing to unpack .../5-qt5-qmake_5.15.13+dfsg-4+rpi1_armhf.deb ...
Unpacking qt5-qmake:armhf (5.15.13+dfsg-4+rpi1) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../6-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libgslcblas0:armhf (2.8+dfsg-3) ...
Setting up qt5-qmake-bin (5.15.13+dfsg-4+rpi1) ...
Setting up libgsl28:armhf (2.8+dfsg-3) ...
Setting up qtchooser (66-2) ...
Setting up libgsl-dev (2.8+dfsg-3) ...
Setting up qt5-qmake:armhf (5.15.13+dfsg-4+rpi1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for man-db (2.12.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for libc-bin (2.38-13+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1+b1 dpkg-dev_1.22.6+rpi1 g++-12_12.4.0-1+rpi1 g++-13_13.3.0-1+rpi1 gcc-12_12.4.0-1+rpi1 gcc-13_13.3.0-1+rpi1 libc6-dev_2.38-13+rpi1 libstdc++-12-dev_12.4.0-1+rpi1 libstdc++-13-dev_13.3.0-1+rpi1 libstdc++6_14-20240221-2.1+rpi1 linux-libc-dev_6.5.6-1+rpi1+b3
Package versions: adduser_3.137 apt_2.9.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-1 autotools-dev_20220109.1 base-files_13.3+rpi1 base-passwd_3.6.4 bash_5.2.21-2.1 binutils_2.41-6+rpi1+b1 binutils-arm-linux-gnueabihf_2.41-6+rpi1+b1 binutils-common_2.41-6+rpi1+b1 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3.1 cpp_4:13.2.0-1+rpi1 cpp-12_12.4.0-1+rpi1 cpp-13_13.3.0-1+rpi1 cpp-13-arm-linux-gnueabihf_13.3.0-1+rpi1 cron_3.0pl1-189 cron-daemon-common_3.0pl1-189 dash_0.5.12-9 dbus_1.14.10-4+b1 dbus-bin_1.14.10-4+b1 dbus-daemon_1.14.10-4+b1 dbus-session-bus-common_1.14.10-4 dbus-system-bus-common_1.14.10-4 debconf_1.5.87 debhelper_13.16 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dmsetup_2:1.02.196-1+b1 dpkg_1.22.6+rpi1 dpkg-dev_1.22.6+rpi1 dwz_0.15-1+b2 e2fsprogs_1.47.1-1 fakeroot_1.33-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:13.2.0-1+rpi1 g++-12_12.4.0-1+rpi1 g++-13_13.3.0-1+rpi1 g++-13-arm-linux-gnueabihf_13.3.0-1+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.4.0-1+rpi1 gcc-12-base_12.4.0-1+rpi1 gcc-13_13.3.0-1+rpi1 gcc-13-arm-linux-gnueabihf_13.3.0-1+rpi1 gcc-13-base_13.3.0-1+rpi1 gcc-14-base_14-20240221-2.1+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+b1 gettext_0.22.5-1 gettext-base_0.22.5-1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+rpi1 libalgorithm-diff-perl_1.201-1 libalgorithm-merge-perl_0.08-5 libapparmor1_3.1.7-1 libapt-pkg6.0t64_2.9.6 libarchive-cpio-perl_0.10-3 libarchive-zip-perl_1.68-1 libasan8_14-20240221-2.1+rpi1 libassuan0_2.5.6-1 libatomic1_14-20240221-2.1+rpi1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-4 libaudit1_1:3.1.2-4 libbinutils_2.41-6+rpi1+b1 libblkid1_2.40.2-1 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-13+rpi1 libc-dev-bin_2.38-13+rpi1 libc6_2.38-13+rpi1 libc6-dev_2.38-13+rpi1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14-20240221-2.1+rpi1 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.7.2-2+rpi1 libctf-nobfd0_2.41-6+rpi1+b1 libctf0_2.41-6+rpi1+b1 libdb5.3t64_5.3.28+dfsg2-7 libdbus-1-3_1.14.10-4+b1 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdevmapper1.02.1_2:1.02.196-1+b1 libdpkg-perl_1.22.6+rpi1 libelf1t64_0.191-1+rpi1 libexpat1_2.6.2-1 libext2fs2t64_1.47.1-1 libfakeroot_1.33-1 libfdisk1_2.40.2-1 libffi8_3.4.6-1 libfile-fcntllock-perl_0.22-4+b3 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-12-dev_12.4.0-1+rpi1 libgcc-13-dev_13.3.0-1+rpi1 libgcc-s1_14-20240221-2.1+rpi1 libgcrypt20_1.11.0-2 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp10_2:6.3.0+dfsg-2 libgnutls30t64_3.8.6-2 libgomp1_14-20240221-2.1+rpi1 libgpg-error0_1.49-2 libgsl-dev_2.8+dfsg-3 libgsl28_2.8+dfsg-3 libgslcblas0_2.8+dfsg-3 libhogweed6t64_3.10-1 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.26-3 libjansson4_2.14-2 libjson-c5_0.17-1 libk5crypto3_1.21.2-1 libkeyutils1_1.6.3-3 libkmod2_31+20240202-2+rpi1 libkrb5support0_1.21.2-1 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-2 libltdl-dev_2.4.7-7+b1 libltdl7_2.4.7-7+b1 liblz4-1_1.9.4-2+rpi1 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmail-sendmail-perl_0.80-3 libmd0_1.1.0-2 libmount1_2.40.2-1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnpth0t64_1.6-3.1 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libpipeline1_1.5.7-2 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1+rpi1+b1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b1 libsepol2_3.5-2+b1 libsframe1_2.41-6+rpi1+b1 libsmartcols1_2.40.2-1 libsqlite3-0_3.46.0-1 libss2_1.47.1-1 libssl3t64_3.2.2-1 libstdc++-12-dev_12.4.0-1+rpi1 libstdc++-13-dev_13.3.0-1+rpi1 libstdc++6_14-20240221-2.1+rpi1 libsys-hostname-long-perl_1.5-3 libsystemd-shared_255.3-1+rpi1+b1 libsystemd0_255.3-1+rpi1+b1 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtirpc-common_1.3.4+ds-1.3 libtool_2.4.7-7 libubsan1_14-20240221-2.1+rpi1 libuchardet0_0.0.8-1 libudev1_255.3-1+rpi1+b1 libunistring5_1.2-1 libuuid1_2.40.2-1 libxml2_2.9.14+dfsg-1.3+b4 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.5.6-1+rpi1+b3 login_1:4.15.3-2 logsave_1.47.1-1 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-2 mawk_1.3.4.20240622-2 mount_2.40.2-1 nano_8.1-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openssl_3.2.2-1 passwd_1:4.15.3-2 patch_2.7.6-7 perl_5.38.2-5 perl-base_5.38.2-5 perl-modules-5.38_5.38.2-5 pinentry-curses_1.2.1-3+b1 po-debconf_1.0.21+nmu1 qt5-qmake_5.15.13+dfsg-4+rpi1 qt5-qmake-bin_5.15.13+dfsg-4+rpi1 qtchooser_66-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 systemd_255.3-1+rpi1+b1 systemd-dev_255.3-1+rpi1 systemd-timesyncd_255.3-1+rpi1+b1 sysvinit-utils_3.09-2 tar_1.35+dfsg-3 tzdata_2024a-4 usr-is-merged_39 util-linux_2.40.2-1 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: clonalframe
Binary: clonalframe
Architecture: any
Version: 1.2-11
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/clonalframe
Vcs-Git: https://salsa.debian.org/med-team/clonalframe.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), qt5-qmake, libgsl-dev
Package-List:
clonalframe deb science optional arch=any
Checksums-Sha1:
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017bfde5f3b92d9c33bbb5a7cfb8636a36189ea1 5956 clonalframe_1.2-11.debian.tar.xz
Checksums-Sha256:
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0f7fa4fb3ba5101ef812f1e10ab56881dfbe4bfaf577fd19199b3475a1e215e6 5956 clonalframe_1.2-11.debian.tar.xz
Files:
ee75640b1ea5dcf9aca0d732f55817c9 45475 clonalframe_1.2.orig.tar.gz
bc01fde45a9756e924e16feb1949080c 5956 clonalframe_1.2-11.debian.tar.xz
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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: cannot verify inline signature for ./clonalframe_1.2-11.dsc: no acceptable signature found
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 disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.2-11+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-98bfe556-22ff-4e9f-a367-b805017e7a33
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package clonalframe
dpkg-buildpackage: info: source version 1.2-11+b2
dpkg-buildpackage: info: source distribution trixie-staging
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
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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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive" dh_auto_configure
qmake -makefile "QMAKE_CFLAGS_RELEASE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
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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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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");
| ^~
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++) {
| ~^~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
In file included from /usr/include/c++/13/bits/specfun.h:43,
from /usr/include/c++/13/cmath:3699,
from /usr/include/c++/13/math.h:36,
from /usr/include/gsl/gsl_math.h:22,
from src/alignment.h:25,
from src/burst.h:24,
from src/burst.cpp:20:
In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]’,
inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]’ at /usr/include/c++/13/bits/stl_algobase.h:506:30,
inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]’ at /usr/include/c++/13/bits/stl_algobase.h:533:42,
inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = int*]’ at /usr/include/c++/13/bits/stl_algobase.h:540:31,
inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = int*]’ at /usr/include/c++/13/bits/stl_algobase.h:633:7,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, std::vector<int> >; _ForwardIterator = int*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:147:27,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _ForwardIterator = int*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/13/bits/stl_vector.h:606:31,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector<int>; _Args = {const std::vector<int, std::allocator<int> >&}; _Tp = std::vector<int>]’ at /usr/include/c++/13/bits/new_allocator.h:191:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector<int>; _Args = {const std::vector<int, std::allocator<int> >&}; _Tp = std::vector<int>]’ at /usr/include/c++/13/bits/alloc_traits.h:538:17,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector<int>; _Alloc = std::allocator<std::vector<int> >]’ at /usr/include/c++/13/bits/stl_vector.h:1286:30,
inlined from ‘std::vector<std::vector<int> >* wb::Burst::makeClusters(std::vector<int>*, gsl_vector_int*, int, bool)’ at src/burst.cpp:299:67:
/usr/include/c++/13/bits/stl_algobase.h:437:30: warning: ‘void* __builtin_memmove(void*, const void*, unsigned int)’ forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=]
437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
| ~^~~~~~~~~~~~~~~~~
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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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) {}
| ~~~~~~~~^
In file included from /usr/include/stdio.h:964,
from /usr/include/gsl/gsl_errno.h:23,
from /usr/include/gsl/gsl_matrix_complex_long_double.h:25,
from /usr/include/gsl/gsl_matrix.h:4,
from src/alignment.h:24,
from src/move.h:23,
from src/move_hidden.h:23,
from src/move_hidden.cpp:20:
In function ‘int printf(const char*, ...)’,
inlined from ‘int wb::Move_hidden::setState(wb::Tree*, wb::Param*, int, gsl_vector*)’ at src/move_hidden.cpp:263:19:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:86:23: warning: ‘r’ may be used uninitialized [-Wmaybe-uninitialized]
86 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/move_hidden.cpp: In member function ‘int wb::Move_hidden::setState(wb::Tree*, wb::Param*, int, gsl_vector*)’:
src/move_hidden.cpp:244:16: note: ‘r’ was declared here
244 | double r;
| ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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:223:29: warning: ‘vals[5]’ may be used uninitialized [-Wmaybe-uninitialized]
223 | {ret+=vals[5];p->rec++;}
| ~~~^~~~~~~~~
src/tree.cpp:197:20: note: ‘vals[5]’ was declared here
197 | double vals[10];
| ^~~~
src/tree.cpp:229:87: warning: ‘vals[9]’ may be used uninitialized [-Wmaybe-uninitialized]
229 | } else if (gsl_vector_char_get(recMap,i)==0) {ret+=vals[8];} else {ret+=vals[9];p->rec++;}
| ~~~^~~~~~~~~
src/tree.cpp:197:20: note: ‘vals[9]’ was declared here
197 | double vals[10];
| ^~~~
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: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-11+b2_armhf.deb'.
dpkg-deb: building package 'clonalframe' in '../clonalframe_1.2-11+b2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../clonalframe_1.2-11+b2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../clonalframe_1.2-11+b2_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 2024-08-05T18:31:38Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalframe_1.2-11+b2_armhf.changes:
------------------------------------
Format: 1.8
Date: Mon, 05 Aug 2024 18:31:26 +0000
Source: clonalframe (1.2-11)
Binary: clonalframe clonalframe-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.2-11+b2
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Raspbian pi5 test autobuilder <root@raspbian.org>
Description:
clonalframe - inference of bacterial microevolution using multilocus sequence d
Changes:
clonalframe (1.2-11+b2) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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b02c941ebc8221d10e91129fd398d6f83add8f10 5522 clonalframe_1.2-11+b2_armhf.buildinfo
fae23388f7eb143103d5f76b147f54dff7b253a4 43500 clonalframe_1.2-11+b2_armhf.deb
Checksums-Sha256:
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f82c6c99347f661d2d021e51c8f09d5dfa78d0a05b42793e4304868b72b296f5 5522 clonalframe_1.2-11+b2_armhf.buildinfo
042a4439c685d64810c4a31fa3cfb65b66ea4cf45362f14c02b24df37e8bcd91 43500 clonalframe_1.2-11+b2_armhf.deb
Files:
abfff2fac54372f831adfbfba66eaede 275820 debug optional clonalframe-dbgsym_1.2-11+b2_armhf.deb
0ab4a99361057a26dffe856580734a38 5522 science optional clonalframe_1.2-11+b2_armhf.buildinfo
8757bf0fd5532a80f80dc889ed0aa047 43500 science optional clonalframe_1.2-11+b2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: clonalframe (1.2-11)
Binary: clonalframe clonalframe-dbgsym
Architecture: armhf
Version: 1.2-11+b2
Binary-Only-Changes:
clonalframe (1.2-11+b2) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi5 test autobuilder <root@raspbian.org> Mon, 05 Aug 2024 18:31:26 +0000
Checksums-Md5:
abfff2fac54372f831adfbfba66eaede 275820 clonalframe-dbgsym_1.2-11+b2_armhf.deb
8757bf0fd5532a80f80dc889ed0aa047 43500 clonalframe_1.2-11+b2_armhf.deb
Checksums-Sha1:
875a1ad32e17743b29cef53be27c617400678235 275820 clonalframe-dbgsym_1.2-11+b2_armhf.deb
fae23388f7eb143103d5f76b147f54dff7b253a4 43500 clonalframe_1.2-11+b2_armhf.deb
Checksums-Sha256:
8b92a715b9cdb50912830dbbd3dd137f7311baf6e4dca1abeee478f4d66e8990 275820 clonalframe-dbgsym_1.2-11+b2_armhf.deb
042a4439c685d64810c4a31fa3cfb65b66ea4cf45362f14c02b24df37e8bcd91 43500 clonalframe_1.2-11+b2_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 05 Aug 2024 18:31:38 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.22.5-1),
autotools-dev (= 20220109.1),
base-files (= 13.3+rpi1),
base-passwd (= 3.6.4),
bash (= 5.2.21-2.1),
binutils (= 2.41-6+rpi1+b1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1+b1),
binutils-common (= 2.41-6+rpi1+b1),
bsdextrautils (= 2.40.2-1),
bsdutils (= 1:2.40.2-1),
build-essential (= 12.10),
bzip2 (= 1.0.8-5.1),
coreutils (= 9.4-3.1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.4.0-1+rpi1),
cpp-13 (= 13.3.0-1+rpi1),
cpp-13-arm-linux-gnueabihf (= 13.3.0-1+rpi1),
dash (= 0.5.12-9),
debconf (= 1.5.87),
debhelper (= 13.16),
debianutils (= 5.20),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.14.0-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.6+rpi1),
dpkg-dev (= 1.22.6+rpi1),
dwz (= 0.15-1+b2),
file (= 1:5.45-3),
findutils (= 4.10.0-2),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.3.0-1+rpi1),
g++-13-arm-linux-gnueabihf (= 13.3.0-1+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.4.0-1+rpi1),
gcc-12-base (= 12.4.0-1+rpi1),
gcc-13 (= 13.3.0-1+rpi1),
gcc-13-arm-linux-gnueabihf (= 13.3.0-1+rpi1),
gcc-13-base (= 13.3.0-1+rpi1),
gcc-14-base (= 14-20240221-2.1+rpi1),
gettext (= 0.22.5-1),
gettext-base (= 0.22.5-1),
grep (= 3.11-4),
groff-base (= 1.23.0-5),
gzip (= 1.12-1.1),
hostname (= 3.23+nmu2),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.2-2+rpi1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 14-20240221-2.1+rpi1),
libatomic1 (= 14-20240221-2.1+rpi1),
libattr1 (= 1:2.5.2-1),
libaudit-common (= 1:3.1.2-4),
libaudit1 (= 1:3.1.2-4),
libbinutils (= 2.41-6+rpi1+b1),
libblkid1 (= 2.40.2-1),
libbz2-1.0 (= 1.0.8-5.1),
libc-bin (= 2.38-13+rpi1),
libc-dev-bin (= 2.38-13+rpi1),
libc6 (= 2.38-13+rpi1),
libc6-dev (= 2.38-13+rpi1),
libcap-ng0 (= 0.8.5-1),
libcap2 (= 1:2.66-5),
libcc1-0 (= 14-20240221-2.1+rpi1),
libcrypt-dev (= 1:4.4.36-4),
libcrypt1 (= 1:4.4.36-4),
libctf-nobfd0 (= 2.41-6+rpi1+b1),
libctf0 (= 2.41-6+rpi1+b1),
libdb5.3t64 (= 5.3.28+dfsg2-7),
libdebconfclient0 (= 0.272),
libdebhelper-perl (= 13.16),
libdpkg-perl (= 1.22.6+rpi1),
libelf1t64 (= 0.191-1+rpi1),
libfile-stripnondeterminism-perl (= 1.14.0-1),
libgcc-12-dev (= 12.4.0-1+rpi1),
libgcc-13-dev (= 13.3.0-1+rpi1),
libgcc-s1 (= 14-20240221-2.1+rpi1),
libgcrypt20 (= 1.11.0-2),
libgdbm-compat4t64 (= 1.23-6),
libgdbm6t64 (= 1.23-6),
libgmp10 (= 2:6.3.0+dfsg-2),
libgomp1 (= 14-20240221-2.1+rpi1),
libgpg-error0 (= 1.49-2),
libgsl-dev (= 2.8+dfsg-3),
libgsl28 (= 2.8+dfsg-3),
libgslcblas0 (= 2.8+dfsg-3),
libicu72 (= 72.1-5),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
liblz4-1 (= 1.9.4-2+rpi1),
liblzma5 (= 5.6.2-2),
libmagic-mgc (= 1:5.45-3),
libmagic1t64 (= 1:5.45-3),
libmd0 (= 1.1.0-2),
libmount1 (= 2.40.2-1),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libpam-modules (= 1.5.3-7),
libpam-modules-bin (= 1.5.3-7),
libpam-runtime (= 1.5.3-7),
libpam0g (= 1.5.3-7),
libpcre2-8-0 (= 10.42-4+b1),
libperl5.38t64 (= 5.38.2-5),
libpipeline1 (= 1.5.7-2),
libseccomp2 (= 2.5.5-1+rpi1+b1),
libselinux1 (= 3.5-2+b2),
libsframe1 (= 2.41-6+rpi1+b1),
libsmartcols1 (= 2.40.2-1),
libssl3t64 (= 3.2.2-1),
libstdc++-13-dev (= 13.3.0-1+rpi1),
libstdc++6 (= 14-20240221-2.1+rpi1),
libsystemd0 (= 255.3-1+rpi1+b1),
libtinfo6 (= 6.5-2),
libtool (= 2.4.7-7),
libubsan1 (= 14-20240221-2.1+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 255.3-1+rpi1+b1),
libunistring5 (= 1.2-1),
libuuid1 (= 2.40.2-1),
libxml2 (= 2.9.14+dfsg-1.3+b4),
libzstd1 (= 1.5.6+dfsg-1),
linux-libc-dev (= 6.5.6-1+rpi1+b3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.1-2),
mawk (= 1.3.4.20240622-2),
ncurses-base (= 6.5-2),
ncurses-bin (= 6.5-2),
patch (= 2.7.6-7),
perl (= 5.38.2-5),
perl-base (= 5.38.2-5),
perl-modules-5.38 (= 5.38.2-5),
po-debconf (= 1.0.21+nmu1),
qt5-qmake (= 5.15.13+dfsg-4+rpi1),
qt5-qmake-bin (= 5.15.13+dfsg-4+rpi1),
qtchooser (= 66-2),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-2),
sensible-utils (= 0.0.24),
sysvinit-utils (= 3.09-2),
tar (= 1.35+dfsg-3),
usr-is-merged (= 39),
util-linux (= 2.40.2-1),
xz-utils (= 5.6.2-2),
zlib1g (= 1:1.3.dfsg+really1.3.1-1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1722882686"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalframe-dbgsym_1.2-11+b2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 275820 bytes: control archive=540 bytes.
399 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clonalframe-dbgsym
Source: clonalframe (1.2-11)
Version: 1.2-11+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 300
Depends: clonalframe (= 1.2-11+b2)
Section: debug
Priority: optional
Description: debug symbols for clonalframe
Build-Ids: 8baf23efd71733f1de4ef63d951206fa31f57855
drwxr-xr-x root/root 0 2024-08-05 18:31 ./
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/lib/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/lib/debug/.build-id/8b/
-rw-r--r-- root/root 296316 2024-08-05 18:31 ./usr/lib/debug/.build-id/8b/af23efd71733f1de4ef63d951206fa31f57855.debug
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/share/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-08-05 18:31 ./usr/share/doc/clonalframe-dbgsym -> clonalframe
clonalframe_1.2-11+b2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 43500 bytes: control archive=1272 bytes.
1267 bytes, 24 lines control
663 bytes, 9 lines md5sums
Package: clonalframe
Source: clonalframe (1.2-11)
Version: 1.2-11+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 114
Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.5), libgsl28 (>= 2.8+dfsg), libstdc++6 (>= 13.1)
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 2024-08-05 18:31 ./
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/bin/
-rwxr-xr-x root/root 95752 2024-08-05 18:31 ./usr/bin/ClonalFrame
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/share/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./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 217 2024-08-05 18:31 ./usr/share/doc/clonalframe/changelog.Debian.armhf.gz
-rw-r--r-- root/root 661 2024-08-05 18:31 ./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 2024-08-05 18:31 ./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 2024-08-05 18:31 ./usr/share/man/
drwxr-xr-x root/root 0 2024-08-05 18:31 ./usr/share/man/man1/
-rw-r--r-- root/root 1055 2024-08-05 18:31 ./usr/share/man/man1/ClonalFrame.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 4416
Build-Time: 11
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 7
Job: clonalframe_1.2-11
Machine Architecture: arm64
Package: clonalframe
Package-Time: 27
Source-Version: 1.2-11
Space: 4416
Status: successful
Version: 1.2-11+b2
--------------------------------------------------------------------------------
Finished at 2024-08-05T18:31:38Z
Build needed 00:00:27, 4416k disk space