Sun Nov 24 10:34:33 UTC 2024 I: starting to build clonalframe/unstable/armhf on jenkins on '2024-11-24 10:34'
Sun Nov 24 10:34:33 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_3/9993/console.log
Sun Nov 24 10:34:33 UTC 2024 I: Downloading source for unstable/clonalframe=1.2-11
--2024-11-24 10:34:33-- http://deb.debian.org/debian/pool/main/c/clonalframe/clonalframe_1.2-11.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2023 (2.0K) [text/prs.lines.tag]
Saving to: ‘clonalframe_1.2-11.dsc’
0K . 100% 266M=0s
2024-11-24 10:34:33 (266 MB/s) - ‘clonalframe_1.2-11.dsc’ saved [2023/2023]
Sun Nov 24 10:34:33 UTC 2024 I: clonalframe_1.2-11.dsc
-----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:
3e107ba13c13cc6bce1531b66a4e337dc4e30675 45475 clonalframe_1.2.orig.tar.gz
017bfde5f3b92d9c33bbb5a7cfb8636a36189ea1 5956 clonalframe_1.2-11.debian.tar.xz
Checksums-Sha256:
eded106eb6193acd47eef20ae43d6cdcf64ca26aee89f7d81f49d894847f1b67 45475 clonalframe_1.2.orig.tar.gz
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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Sun Nov 24 10:34:33 UTC 2024 I: Checking whether the package is not for us
Sun Nov 24 10:34:33 UTC 2024 I: Starting 1st build on remote node ff4a-armhf-rb.debian.net.
Sun Nov 24 10:34:33 UTC 2024 I: Preparing to do remote build '1' on ff4a-armhf-rb.debian.net.
Sun Nov 24 10:36:27 UTC 2024 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Nov 23 22:34:40 -12 2024
I: pbuilder-time-stamp: 1732444480
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [clonalframe_1.2-11.dsc]
I: copying [./clonalframe_1.2.orig.tar.gz]
I: copying [./clonalframe_1.2-11.debian.tar.xz]
I: Extracting source
gpgv: Signature made Mon Sep 27 19:36:29 2021
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 clonalframe-1.2
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
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/5168/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='47007943227b4da7bcfad44f8f703e12'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='5168'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.eHGONq7W/pbuilderrc_61cr --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eHGONq7W/b1 --logfile b1/build.log clonalframe_1.2-11.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux ff4a 6.1.0-27-armmp-lpae #1 SMP Debian 6.1.115-1 (2024-11-01) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/5168/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), qt5-qmake, libgsl-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19686 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on qt5-qmake; however:
Package qt5-qmake is not installed.
pbuilder-satisfydepends-dummy depends on libgsl-dev; however:
Package libgsl-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} qt5-qmake{a} qt5-qmake-bin{a} qtchooser{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.2 MB of archives. After unpacking 81.9 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 23 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf libgslcblas0 armhf 2.8+dfsg-5 [85.5 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf libgsl28 armhf 2.8+dfsg-5 [812 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf libgsl-dev armhf 2.8+dfsg-5 [1030 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf qt5-qmake-bin armhf 5.15.15+dfsg-2 [914 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf qtchooser armhf 66-2 [23.6 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf qt5-qmake armhf 5.15.15+dfsg-2 [224 kB]
Fetched 22.2 MB in 2s (13.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
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(Reading database ... 19686 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:armhf.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ...
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Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ...
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Unpacking libuchardet0:armhf (0.0.8-1+b2) ...
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Preparing to unpack .../06-groff-base_1.23.0-5_armhf.deb ...
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Unpacking man-db (2.13.0-1) ...
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Setting up libpipeline1:armhf (1.5.8-1) ...
Setting up libicu72:armhf (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-11) ...
Setting up libgslcblas0:armhf (2.8+dfsg-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.20) ...
Setting up libmagic1t64:armhf (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-2) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:armhf (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up qt5-qmake-bin (5.15.15+dfsg-2) ...
Setting up autopoint (0.22.5-2) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b2) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:armhf (0.0.8-1+b2) ...
Setting up libgsl28:armhf (2.8+dfsg-5) ...
Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up qtchooser (66-2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.22.5-2) ...
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Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/clonalframe-1.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../clonalframe_1.2-11_source.changes
dpkg-buildpackage: info: source package clonalframe
dpkg-buildpackage: info: source version 1.2-11
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
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 '/build/reproducible-path/clonalframe-1.2'
dh_clean
rm -rf bin build Makefile
make[1]: Leaving directory '/build/reproducible-path/clonalframe-1.2'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/clonalframe-1.2'
QT_SELECT=5 CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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 /build/reproducible-path/clonalframe-1.2/.qmake.stash
make[1]: Leaving directory '/build/reproducible-path/clonalframe-1.2'
dh_auto_build
make -j3
make[1]: Entering directory '/build/reproducible-path/clonalframe-1.2'
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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
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=/build/reproducible-path/clonalframe-1.2=. -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_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=/build/reproducible-path/clonalframe-1.2=. -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
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -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
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=/build/reproducible-path/clonalframe-1.2=. -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
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -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/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=/build/reproducible-path/clonalframe-1.2=. -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
In file included from /usr/include/c++/14/bits/specfun.h:43,
from /usr/include/c++/14/cmath:3898,
from /usr/include/c++/14/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++/14/bits/stl_algobase.h:521:30,
inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42,
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++/14/bits/stl_algobase.h:555:31,
inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7,
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++/14/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++/14/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++/14/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++/14/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++/14/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++/14/bits/alloc_traits.h:569:17,
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++/14/bits/stl_vector.h:1288:30,
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++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=]
452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -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
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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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
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=/build/reproducible-path/clonalframe-1.2=. -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
In file included from /usr/include/stdio.h:970,
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:118:23: warning: 'r' may be used uninitialized [-Wmaybe-uninitialized]
118 | 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=/build/reproducible-path/clonalframe-1.2=. -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) {}
| ~~~~~~~~^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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
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)
| ^
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)
| ~~~~~~~~^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -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_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=/build/reproducible-path/clonalframe-1.2=. -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
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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=/build/reproducible-path/clonalframe-1.2=. -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/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/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=/build/reproducible-path/clonalframe-1.2=. -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 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 '/build/reproducible-path/clonalframe-1.2'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/clonalframe/
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
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
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-11_armhf.deb'.
dpkg-deb: building package 'clonalframe' in '../clonalframe_1.2-11_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../clonalframe_1.2-11_armhf.buildinfo
dpkg-genchanges --build=binary -O../clonalframe_1.2-11_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/5168 and its subdirectories
I: Current time: Sat Nov 23 22:36:22 -12 2024
I: pbuilder-time-stamp: 1732444582
Sun Nov 24 10:36:30 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64z-armhf-rb.debian.net.
Sun Nov 24 10:36:30 UTC 2024 I: Preparing to do remote build '2' on virt64z-armhf-rb.debian.net.
Sun Nov 24 10:37:32 UTC 2024 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net.
Sun Nov 24 10:37:35 UTC 2024 I: 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: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.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:
f2423319524ff0b4b7e107156b7a1cc5b930cd62 277688 clonalframe-dbgsym_1.2-11_armhf.deb
003ae17d716329945b3ce1c78783a580573dea56 4996 clonalframe_1.2-11_armhf.buildinfo
10a18607f91c65e5977d1e3e81ca749a6c9c5c3e 42804 clonalframe_1.2-11_armhf.deb
Checksums-Sha256:
717b8e9e3f6d78c641ff610c141ded2b2ab6f04dc7f3e1cde01a053b9bb22b07 277688 clonalframe-dbgsym_1.2-11_armhf.deb
cabed7390186a1cf5280f69fee20a45af95d842042a185e795360ad4ba18cc85 4996 clonalframe_1.2-11_armhf.buildinfo
1983a20e09305c4ac33c8d6e52b1bb36c8c5faccef66270d13934cb2d99a5053 42804 clonalframe_1.2-11_armhf.deb
Files:
38df9faab0b6c00cc480f3c952d6ea91 277688 debug optional clonalframe-dbgsym_1.2-11_armhf.deb
9af1f2ba5325295d78fa8249f07e2eae 4996 science optional clonalframe_1.2-11_armhf.buildinfo
94f1d92a8c468565ce288c2c8a83e84f 42804 science optional clonalframe_1.2-11_armhf.deb
Sun Nov 24 10:37:36 UTC 2024 I: diffoscope 283 will be used to compare the two builds:
Running as unit: rb-diffoscope-armhf_3-9993.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.eHGONq7W/clonalframe_1.2-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.eHGONq7W/clonalframe_1.2-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.eHGONq7W/clonalframe_1.2-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.eHGONq7W/b1/clonalframe_1.2-11_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.eHGONq7W/b2/clonalframe_1.2-11_armhf.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.360s)
0.360s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.025s)
0.025s 12 calls diffoscope.comparators.binary.FilesystemFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 795ms
CPU time consumed: 785ms
Sun Nov 24 10:37:37 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists.
Sun Nov 24 10:37:37 UTC 2024 I: clonalframe from unstable built successfully and reproducibly on armhf.
Sun Nov 24 10:37:39 UTC 2024 I: Submitting .buildinfo files to external archives:
Sun Nov 24 10:37:39 UTC 2024 I: Submitting 8.0K b1/clonalframe_1.2-11_armhf.buildinfo.asc
Sun Nov 24 10:37:40 UTC 2024 I: Submitting 8.0K b2/clonalframe_1.2-11_armhf.buildinfo.asc
Sun Nov 24 10:37:41 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Nov 24 10:37:41 UTC 2024 I: Done submitting .buildinfo files.
Sun Nov 24 10:37:41 UTC 2024 I: Removing signed clonalframe_1.2-11_armhf.buildinfo.asc files:
removed './b1/clonalframe_1.2-11_armhf.buildinfo.asc'
removed './b2/clonalframe_1.2-11_armhf.buildinfo.asc'