Diff of the two buildlogs: -- --- b1/build.log 2025-01-09 08:58:26.689525062 +0000 +++ b2/build.log 2025-01-09 09:06:17.324133811 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jan 8 20:50:21 -12 2025 -I: pbuilder-time-stamp: 1736412621 +I: Current time: Thu Jan 9 22:59:07 +14 2025 +I: pbuilder-time-stamp: 1736413147 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying qt5.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4964/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3788/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 9 08:59 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3788/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3788/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='38eabf3da2304aaa82271f9acd4ac123' - 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='4964' - PS1='# ' - PS2='> ' + INVOCATION_ID=6ebf1e38ce6a4197abc1fb12e8bd020f + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3788 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.eAvW2AA4/pbuilderrc_piTN --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.eAvW2AA4/b1 --logfile b1/build.log clustalx_2.1+lgpl-9.dsc' - SUDO_GID='112' - SUDO_UID='106' - 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/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.eAvW2AA4/pbuilderrc_1lN8 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eAvW2AA4/b2 --logfile b2/build.log clustalx_2.1+lgpl-9.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32b 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4964/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3788/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -312,7 +344,7 @@ Get: 197 http://deb.debian.org/debian unstable/main armhf qtbase5-dev-tools armhf 5.15.15+dfsg-2 [659 kB] Get: 198 http://deb.debian.org/debian unstable/main armhf qtbase5-dev armhf 5.15.15+dfsg-2 [1070 kB] Get: 199 http://deb.debian.org/debian unstable/main armhf qttools5-dev-tools armhf 5.15.15-4 [922 kB] -Fetched 125 MB in 2s (66.8 MB/s) +Fetched 125 MB in 2s (59.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libglvnd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19561 files and directories currently installed.) @@ -973,8 +1005,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jan 9 08:51:35 UTC 2025. -Universal Time is now: Thu Jan 9 08:51:35 UTC 2025. +Local time is now: Thu Jan 9 09:00:44 UTC 2025. +Universal Time is now: Thu Jan 9 09:00:44 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libcap2-bin (1:2.66-5+b1) ... @@ -1140,7 +1172,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/clustalx-2.1+lgpl/ && 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 > ../clustalx_2.1+lgpl-9_source.changes +I: user script /srv/workspace/pbuilder/3788/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3788/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/clustalx-2.1+lgpl/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../clustalx_2.1+lgpl-9_source.changes dpkg-buildpackage: info: source package clustalx dpkg-buildpackage: info: source version 2.1+lgpl-9 dpkg-buildpackage: info: source distribution unstable @@ -1170,11 +1206,12 @@ -e "s:LFLAGS *= .*:& -Wl,-z,relro -Wl,-z,now:" Makefile make[1]: Leaving directory '/build/reproducible-path/clustalx-2.1+lgpl' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/reproducible-path/clustalx-2.1+lgpl' g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignmentWidget.o AlignmentWidget.cpp In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from AlignmentParameters.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -1189,98 +1226,6 @@ | ~~~~~~~~~~~~^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from AlignmentViewerWidget.h:36, - from AlignmentViewerWidget.cpp:66: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qvarlengtharray.h:52, - from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qmetatype.h:48, - from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qobject.h:54, - from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qabstractanimation.h:43, - from /usr/include/arm-linux-gnueabihf/qt5/QtCore/QtCore:6, - from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 75 | auto_ptr clustalOutFile; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 76 | auto_ptr gcgOutFile; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 77 | auto_ptr nbrfOutFile; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 78 | auto_ptr phylipOutFile; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 79 | auto_ptr gdeOutFile; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 80 | auto_ptr nexusOutFile; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 81 | auto_ptr fastaOutFile; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': -AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 588 | for(i = 0; i < len && i < gapMask->size(); i++) - | ~~^~~~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': -AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 645 | for (i = 0; i < len && i < _secStructMask->size();i++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 652 | for(i = 0; i < len && i < ssMask.size(); i++) - | ~~^~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)': -AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] - 781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) - | ~~~~~~~~~~~~~~~^~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignmentWidget.o AlignmentWidget.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignOutputFileNames.o AlignOutputFileNames.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, from AlignmentWidget.cpp:49: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -1405,46 +1350,113 @@ | ^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from AlignOutputFileNames.h:10, - from AlignOutputFileNames.cpp:26: + from AlignmentViewerWidget.h:36, + from AlignmentViewerWidget.cpp:66: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 106 | auto_ptr outFileNames; - | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); + | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qvarlengtharray.h:52, from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qmetatype.h:48, from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qobject.h:54, - from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qsharedpointer_impl.h:65, - from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/arm-linux-gnueabihf/qt5/QtGui/qpixmap.h:48, - from /usr/include/arm-linux-gnueabihf/qt5/QtGui/qicon.h:46, - from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/QPushButton:1, - from AlignOutputFileNames.cpp:16: + from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qabstractanimation.h:43, + from /usr/include/arm-linux-gnueabihf/qt5/QtCore/QtCore:6, + from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 75 | auto_ptr clustalOutFile; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 76 | auto_ptr gcgOutFile; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 77 | auto_ptr nbrfOutFile; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 78 | auto_ptr phylipOutFile; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 79 | auto_ptr gdeOutFile; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 80 | auto_ptr nexusOutFile; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 81 | auto_ptr fastaOutFile; + | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': +AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 588 | for(i = 0; i < len && i < gapMask->size(); i++) + | ~~^~~~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': +AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 645 | for (i = 0; i < len && i < _secStructMask->size();i++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 652 | for(i = 0; i < len && i < ssMask.size(); i++) + | ~~^~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)': +AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] + 781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) + | ~~~~~~~~~~~~~~~^~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignOutputFileNames.o AlignOutputFileNames.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ColorFileXmlParser.o ColorFileXmlParser.cpp +ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] + 74 | // tr("colorrules not found in the parameter file, using\ + | ^ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, - from BootstrapTreeDialog.h:11, - from BootstrapTreeDialog.cpp:18: + from AlignOutputFileNames.h:10, + from AlignOutputFileNames.cpp:26: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 70 | auto_ptr treeFileNames; +AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 106 | auto_ptr outFileNames; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qvarlengtharray.h:52, @@ -1457,16 +1469,10 @@ from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/QPushButton:1, - from BootstrapTreeDialog.cpp:8: + from AlignOutputFileNames.cpp:16: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ColorFileXmlParser.o ColorFileXmlParser.cpp -ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] - 74 | // tr("colorrules not found in the parameter file, using\ - | ^ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1517,7 +1523,36 @@ ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 251 | if(colorNum > 0 && colorNum - 1 < colorPar.size()) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from BootstrapTreeDialog.h:11, + from BootstrapTreeDialog.cpp:18: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 70 | auto_ptr treeFileNames; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qvarlengtharray.h:52, + from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qmetatype.h:48, + from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qobject.h:54, + from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qsharedpointer_impl.h:65, + from /usr/include/arm-linux-gnueabihf/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/arm-linux-gnueabihf/qt5/QtGui/qpixmap.h:48, + from /usr/include/arm-linux-gnueabihf/qt5/QtGui/qicon.h:46, + from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/arm-linux-gnueabihf/qt5/QtWidgets/QPushButton:1, + from BootstrapTreeDialog.cpp:8: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1543,20 +1578,10 @@ ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] 175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from ColumnScoreParams.cpp:23: -clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)': -ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] - 51 | void ColumnScoreParams::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1568,8 +1593,19 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp +In file included from clustalW/substitutionMatrix/globalmatrix.h:8, + from ColumnScoreParams.cpp:23: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)': +ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] + 51 | void ColumnScoreParams::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1582,6 +1618,7 @@ 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o main.o main.cpp HelpDisplayWidget.cpp: In member function 'std::string* HelpDisplayWidget::loadHelpInformation(char)': HelpDisplayWidget.cpp:147:29: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 147 | catch(ifstream::failure e) @@ -1614,20 +1651,6 @@ /usr/include/arm-linux-gnueabihf/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o main.o main.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp -In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from LowScoringSegParams.cpp:22: -clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': -LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] - 51 | void LowScoringSegParams::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ In file included from main.cpp:21: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); @@ -1707,8 +1730,34 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp +In file included from clustalW/substitutionMatrix/globalmatrix.h:8, + from LowScoringSegParams.cpp:22: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': +LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] + 51 | void LowScoringSegParams::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from PostscriptFileParams.h:4, + from PostscriptFileParams.cpp:1: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, @@ -1810,9 +1859,17 @@ TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 73 | auto_ptr treeFileNames; | ^~~~~~~~ +In file included from clustalW/substitutionMatrix/globalmatrix.h:8, + from PairwiseParams.cpp:23: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ In file included from mainwindow.cpp:102: BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr treeFileNames; @@ -1820,6 +1877,10 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +PairwiseParams.cpp: In member function 'virtual void PairwiseParams::showEvent(QShowEvent*)': +PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] + 74 | void PairwiseParams::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ mainwindow.cpp: In member function 'virtual void MainWindow::showEvent(QShowEvent*)': mainwindow.cpp:198:40: warning: unused parameter 'event' [-Wunused-parameter] 198 | void MainWindow::showEvent(QShowEvent* event) @@ -1828,35 +1889,7 @@ mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] 1454 | void MainWindow::writeViewer1AsPostscript(int type) | ~~~~^~~~ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from PostscriptFileParams.h:4, - from PostscriptFileParams.cpp:1: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp -In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from PairwiseParams.cpp:23: -clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -PairwiseParams.cpp: In member function 'virtual void PairwiseParams::showEvent(QShowEvent*)': -PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] - 74 | void PairwiseParams::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1904,8 +1937,12 @@ PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] 781 | int psX, psY, curveBottom; | ^~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1984,7 +2021,7 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, @@ -2010,9 +2047,9 @@ /usr/include/arm-linux-gnueabihf/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/fileInput/../alignment/Alignment.h:42, from clustalW/fileInput/FileReader.h:12, @@ -2144,6 +2181,7 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -2175,6 +2213,31 @@ | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, + from clustalW/alignment/Alignment.cpp:25: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()': +clustalW/alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 47 | register int sl; /* which have code = gap_pos2 */ + | ^~ +clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()': +clustalW/alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 122 | register int sl; /* which have code = gap_pos2 */ + | ^~ +clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()': +clustalW/alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 617 | register int sl; + | ^~ +clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)': +clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable] + 1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin(); + | ^~~~~~~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from WritePostscriptFile.h:10, from WritePostscriptFile.cpp:24: @@ -2257,37 +2320,9 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from clustalW/alignment/Alignment.cpp:25: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()': -clustalW/alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 47 | register int sl; /* which have code = gap_pos2 */ - | ^~ -clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()': -clustalW/alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 122 | register int sl; /* which have code = gap_pos2 */ - | ^~ -clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()': -clustalW/alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 617 | register int sl; - | ^~ -clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)': -clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable] - 1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin(); - | ^~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, from clustalW/alignment/AlignmentOutput.h:24, from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -2399,6 +2434,8 @@ clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 2351 | catch(VectorOutOfRange e) | ^ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/ObjectiveScore.h:15, from clustalW/alignment/ObjectiveScore.cpp:10: @@ -2408,7 +2445,6 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp @@ -2459,7 +2495,6 @@ 555 | catch(exception ex) | ^~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual std::vector clustalw::MSFFileParser::getSeqRange(int, int, std::string*)': clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter] 34 | vector MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) @@ -2477,6 +2512,7 @@ clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter] 247 | string& secStructName, int &structPenalties, int length) | ~~~~^~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::string*)': @@ -2496,6 +2532,7 @@ clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] 446 | int &structPenalties, int length) | ~~~~^~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp clustalW/fileInput/PIRFileParser.cpp: In member function 'virtual void clustalw::PIRFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] 292 | void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, @@ -2513,10 +2550,6 @@ clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] 240 | void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp clustalW/general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const': clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript 1 is above array bounds of 'char [1]' [-Warray-bounds=] 106 | delim[1] = 0; @@ -2524,6 +2557,10 @@ clustalW/general/ClustalWResources.cpp:104:10: note: while referencing 'delim' 104 | char delim[1]; | ^~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp In file included from clustalW/general/OutputFile.cpp:9: clustalW/general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; @@ -2533,7 +2570,7 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/general/../alignment/Alignment.h:42, from clustalW/general/Stats.cpp:15: @@ -2543,13 +2580,13 @@ clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp clustalW/general/UserParameters.cpp: In constructor 'clustalw::UserParameters::UserParameters(bool)': clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter] 33 | UserParameters::UserParameters(bool log) | ~~~~~^~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp clustalW/general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)': clustalW/general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 475 | register int i; @@ -2566,7 +2603,6 @@ clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] 519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) | ~~~~~~~~^~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp clustalW/general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)': clustalW/general/Utility.cpp:183:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | fgets(line, MAXLINE, stdin); @@ -2575,6 +2611,7 @@ clustalW/general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from clustalW/general/Utility.cpp:18: @@ -2595,28 +2632,6 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from 'double clustalw::Utility::median(std::vector)' at clustalW/general/Utility.cpp:562:14: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from 'double clustalw::Utility::median(std::vector)' at clustalW/general/Utility.cpp:562:14: -/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1822 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/interface/../fileInput/../alignment/Alignment.h:42, from clustalW/interface/../fileInput/FileReader.h:12, @@ -2692,6 +2707,28 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from 'double clustalw::Utility::median(std::vector)' at clustalW/general/Utility.cpp:562:14: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from 'double clustalw::Utility::median(std::vector)' at clustalW/general/Utility.cpp:562:14: +/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1822 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/interface/../fileInput/../alignment/Alignment.h:42, from clustalW/interface/../fileInput/FileReader.h:12, @@ -2704,16 +2741,6 @@ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ @@ -2781,6 +2808,27 @@ clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 41 | catch(bad_alloc) | ^~~~~~~~~ +In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/multipleAlign/../alignment/Alignment.h:42, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()': +clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] + 520 | clustalObj->getHelp('C'); + | ~~~~~~~~~~~~~~~~~~~^~~~~ +clustalW/interface/InteractiveMenu.cpp:521:13: note: here + 521 | case 'Q': + | ^~~~ +clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': +clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1190 | system(lin1.c_str()); + | ~~~~~~^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, @@ -2830,22 +2878,6 @@ clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] 170 | int count; | ^~~~~ -clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()': -clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] - 520 | clustalObj->getHelp('C'); - | ~~~~~~~~~~~~~~~~~~~^~~~~ -clustalW/interface/InteractiveMenu.cpp:521:13: note: here - 521 | case 'Q': - | ^~~~ -clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': -clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1190 | system(lin1.c_str()); - | ~~~~~~^~~~~~~~~~~~~~ -clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 231 | tmpnam (buffer); - | ~~~~~~~^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/LowScoreSegProfile.h:13, @@ -2856,6 +2888,11 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 231 | tmpnam (buffer); + | ~~~~~~~^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, @@ -2875,9 +2912,7 @@ clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] 359 | string phylipName) | ~~~~~~~^~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, @@ -2899,6 +2934,11 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +clustalW/multipleAlign/ProfileBase.cpp: In member function 'void clustalw::ProfileBase::calcResidueSpecificPen(clustalw::SeqArray*, std::vector*)': +clustalW/multipleAlign/ProfileBase.cpp:372:25: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 372 | if ((ix < 0) || (ix > _maxAA)) + | ~~~^~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileStandard.h:9, @@ -2909,12 +2949,10 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/multipleAlign/ProfileBase.cpp: In member function 'void clustalw::ProfileBase::calcResidueSpecificPen(clustalw::SeqArray*, std::vector*)': -clustalW/multipleAlign/ProfileBase.cpp:372:25: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 372 | if ((ix < 0) || (ix > _maxAA)) - | ~~~^~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileWithSub.h:9, @@ -2928,21 +2966,19 @@ In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, - from clustalW/pairwise/FastPairwiseAlign.h:9, - from clustalW/pairwise/FastPairwiseAlign.cpp:10: + from clustalW/pairwise/FullPairwiseAlign.h:9, + from clustalW/pairwise/FullPairwiseAlign.cpp:9: clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, - from clustalW/pairwise/FullPairwiseAlign.h:9, - from clustalW/pairwise/FullPairwiseAlign.cpp:9: + from clustalW/pairwise/FastPairwiseAlign.h:9, + from clustalW/pairwise/FastPairwiseAlign.cpp:10: clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ @@ -2956,7 +2992,6 @@ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::tempInterface(int, int)': clustalW/substitutionMatrix/SubMatrix.cpp:1613:35: warning: unused parameter 'alignResidueType' [-Wunused-parameter] 1613 | void SubMatrix::tempInterface(int alignResidueType, int alignType) @@ -2972,8 +3007,10 @@ clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] 1717 | int maxRes; | ^~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)': clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized] 1103 | return (maxRes); @@ -3023,10 +3060,36 @@ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp +clustalW/tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)': +clustalW/tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 164 | register int i; + | ^ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp +In file included from /usr/include/c++/14/vector:72, + from clustalW/tree/NJTree.h:9, + from clustalW/tree/NJTree.cpp:10: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)' at clustalW/tree/NJTree.cpp:230:31: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)' at clustalW/tree/NJTree.cpp:231:32: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)' at clustalW/tree/NJTree.cpp:233:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/Tree.h:13, @@ -3037,10 +3100,7 @@ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)': -clustalW/tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 164 | register int i; - | ^ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp clustalW/tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^~~~~~~~ @@ -3062,29 +3122,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from clustalW/tree/NJTree.h:9, - from clustalW/tree/NJTree.cpp:10: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)' at clustalW/tree/NJTree.cpp:230:31: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)' at clustalW/tree/NJTree.cpp:231:32: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)' at clustalW/tree/NJTree.cpp:233:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/TreeInterface.h:19, @@ -3249,7 +3286,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, @@ -3279,6 +3315,7 @@ | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/../ClusterTree.h:20, @@ -3290,6 +3327,16 @@ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, + from clustalW/tree/UPGMA/RootedGuideTree.h:17, + from clustalW/tree/UPGMA/RootedGuideTree.cpp:10: +clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ In file included from clustalW/tree/UPGMA/../ClusterTree.h:23: clustalW/tree/UPGMA/../../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; @@ -3340,30 +3387,24 @@ In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, - from clustalW/tree/UPGMA/RootedGuideTree.cpp:10: + from clustalW/tree/UPGMA/RootedTreeOutput.h:15, + from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp g++ -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -dM -E -o moc_predefs.h /usr/lib/arm-linux-gnueabihf/qt5/mkspecs/features/data/dummy.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp -In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, - from clustalW/tree/UPGMA/RootedGuideTree.h:17, - from clustalW/tree/UPGMA/RootedTreeOutput.h:15, - from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include ColumnScoreParams.h -o moc_ColumnScoreParams.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, @@ -3395,11 +3436,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include ColumnScoreParams.h -o moc_ColumnScoreParams.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include FileDialog.h -o moc_FileDialog.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/arm-linux-gnueabihf/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/arm-linux-gnueabihf/14/include -I/usr/local/include -I/usr/include/arm-linux-gnueabihf -I/usr/include HistogramWidget.h -o moc_HistogramWidget.cpp @@ -3418,6 +3454,7 @@ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, @@ -3428,7 +3465,6 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, @@ -3441,6 +3477,8 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3460,8 +3498,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3483,6 +3519,7 @@ | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3496,8 +3533,8 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3509,9 +3546,9 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, @@ -3523,7 +3560,6 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp In file included from clustalW/Clustal.h:18, from mainwindow.h:45: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] @@ -3604,6 +3640,8 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3615,10 +3653,9 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, @@ -3629,7 +3666,6 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -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 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/arm-linux-gnueabihf/qt5 -I/usr/include/arm-linux-gnueabihf/qt5/QtWidgets -I/usr/include/arm-linux-gnueabihf/qt5/QtGui -I/usr/include/arm-linux-gnueabihf/qt5/QtXml -I/usr/include/arm-linux-gnueabihf/qt5/QtCore -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3703,8 +3739,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-9_armhf.deb'. dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-9_armhf.deb'. +dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-9_armhf.deb'. dpkg-genbuildinfo --build=binary -O../clustalx_2.1+lgpl-9_armhf.buildinfo dpkg-genchanges --build=binary -O../clustalx_2.1+lgpl-9_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3712,12 +3748,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3788/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3788/tmp/hooks/B01_cleanup finished 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/4964 and its subdirectories -I: Current time: Wed Jan 8 20:58:18 -12 2025 -I: pbuilder-time-stamp: 1736413098 +I: removing directory /srv/workspace/pbuilder/3788 and its subdirectories +I: Current time: Thu Jan 9 23:06:09 +14 2025 +I: pbuilder-time-stamp: 1736413569