Diff of the two buildlogs: -- --- b1/build.log 2025-02-03 11:54:00.345921090 +0000 +++ b2/build.log 2025-02-03 11:55:28.257954817 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Feb 2 23:52:45 -12 2025 -I: pbuilder-time-stamp: 1738583565 +I: Current time: Mon Mar 9 08:17:03 +14 2026 +I: pbuilder-time-stamp: 1772993823 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/1057078/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1591934/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Mar 8 18:17 /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/1591934/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1591934/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-linux-gnu") + 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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='c09cfab560694311b909adaef729f0dc' - 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='1057078' - PS1='# ' - PS2='> ' + INVOCATION_ID=212ad6f823074d1cb0cba11357867648 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=1591934 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.Qq6bFGfp/pbuilderrc_PUaM --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Qq6bFGfp/b1 --logfile b1/build.log clustalx_2.1+lgpl-9.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.Qq6bFGfp/pbuilderrc_xwVK --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Qq6bFGfp/b2 --logfile b2/build.log clustalx_2.1+lgpl-9.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) 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/1057078/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1591934/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -297,7 +329,7 @@ Get: 182 http://deb.debian.org/debian trixie/main arm64 qtbase5-dev-tools arm64 5.15.15+dfsg-2 [718 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 qtbase5-dev arm64 5.15.15+dfsg-2 [1120 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 qttools5-dev-tools arm64 5.15.15-5 [1003 kB] -Fetched 112 MB in 1s (207 MB/s) +Fetched 112 MB in 0s (251 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19958 files and directories currently installed.) @@ -907,8 +939,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Feb 3 11:53:13 UTC 2025. -Universal Time is now: Mon Feb 3 11:53:13 UTC 2025. +Local time is now: Sun Mar 8 18:17:30 UTC 2026. +Universal Time is now: Sun Mar 8 18:17:30 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -1064,7 +1096,11 @@ 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/1591934/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1591934/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 @@ -1115,7 +1151,8 @@ from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, - from HardCodedColorScheme.cpp:1: + from ColorParameters.h:11, + from ColorParameters.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"); | ^~~~~~~~~~~~~~ @@ -1126,8 +1163,7 @@ from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from ColorParameters.cpp:1: + from HardCodedColorScheme.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"); | ^~~~~~~~~~~~~~ @@ -1174,6 +1210,8 @@ | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1185,8 +1223,6 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1218,6 +1254,60 @@ | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from HardCodedColorScheme.h:8, + from ColorParameters.h:11, + from ColorFileXmlParser.h:9, + from ColorFileXmlParser.cpp:3: +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"); + | ^~~~~~~~~~~~~~ +ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] + 85 | QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ +ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] + 138 | void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ +ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] + 175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ +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: +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 /usr/include/c++/14/memory:78, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qvarlengtharray.h:52, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qmetatype.h:48, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qobject.h:54, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:65, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/aarch64-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QPushButton:1, + from AlignOutputFileNames.cpp:16: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +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] @@ -1263,20 +1353,12 @@ 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; | ^~~~~~~~ -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"); - | ^~~~~~~~~~~~~~ /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; | ^~~~~~~~ -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"); - | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ @@ -1298,39 +1380,7 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -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, - 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"); - | ^~~~~~~~~~~~~~ -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/aarch64-linux-gnu/qt5/QtCore/qvarlengtharray.h:52, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qmetatype.h:48, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qobject.h:54, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:65, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/aarch64-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QPushButton:1, - 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp 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 'long unsigned int'} [-Wsign-compare] 588 | for(i = 0; i < len && i < gapMask->size(); i++) @@ -1346,23 +1396,42 @@ AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] 781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) | ~~~~~~~~~~~~~~~^~~~~ -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] +HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)': +HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 180 | if(column >= 0 && column < arrayOfHeights->size()) + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +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"); | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +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"); | ^~~~~~~~~~~~~~ +HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 198 | if(column >= 0 && column < arrayOfHeights->size()) + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +HistogramWidget.cpp:208:47: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] + 208 | (fontMetrics.width(QString::number(rulerNum))) / 2; + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:50, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qframe.h:44, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qlabel.h:44, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QLabel:1, + from HistogramWidget.h:29, + from HistogramWidget.cpp:23: +/usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here + 106 | int width(const QString &, int len = -1) const; + | ^~~~~ +HistogramWidget.cpp:241:61: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] + 241 | (fontMetrics.width(QString::number(0))) / 2, yPos, boxWidth, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here + 106 | int width(const QString &, int len = -1) const; + | ^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from ColorFileXmlParser.h:9, - from ColorFileXmlParser.cpp:3: + 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] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ @@ -1383,21 +1452,9 @@ AlignmentWidget.cpp:225:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 225 | for(unsigned int j = 0; j < lengthLongestSeq; j++) | ~~^~~~~~~~~~~~~~~~~~ -ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)': -ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] - 85 | QTreeWidgetItem *parentItem) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ -ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)': -ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] - 138 | void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ AlignmentWidget.cpp:235:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 235 | if(code >= 0 && code < conservationPixmaps->size()) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)': -ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] - 175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ AlignmentWidget.cpp:268:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 268 | if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1428,11 +1485,6 @@ AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 569 | if(selectedRes >= selectedColoredRes->size()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()': AlignmentWidget.cpp:689:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 689 | for(int j = 1; j <= strongGroup.size(); j++) @@ -1449,9 +1501,6 @@ AlignmentWidget.cpp:725:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 725 | for(int k = 1; k <= strongGroup.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~~~ -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"); - | ^~~~~~~~~~~~~~ AlignmentWidget.cpp:737:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 737 | for(int k = 1; k <= weakGroup.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~ @@ -1465,10 +1514,6 @@ AlignmentWidget.cpp:878:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 878 | if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentParameters.cpp: In member function 'virtual void AlignmentParameters::showEvent(QShowEvent*)': -AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter] - 48 | void AlignmentParameters::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()': AlignmentWidget.cpp:927:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 927 | if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) @@ -1507,20 +1552,6 @@ /usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ -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) - | ^ -HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] - 61 | int i, number, nlines; - | ^~~~~~ -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"); - | ^~~~~~~~~~~~~~ -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 clustalW/Clustal.h:18, from mainwindow.h:45, from main.cpp:24: @@ -1593,37 +1624,20 @@ /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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp -HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)': -HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 180 | if(column >= 0 && column < arrayOfHeights->size()) - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 198 | if(column >= 0 && column < arrayOfHeights->size()) - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -HistogramWidget.cpp:208:47: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] - 208 | (fontMetrics.width(QString::number(rulerNum))) / 2; - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:50, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qframe.h:44, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qlabel.h:44, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QLabel:1, - from HistogramWidget.h:29, - from HistogramWidget.cpp:23: -/usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here - 106 | int width(const QString &, int len = -1) const; - | ^~~~~ -HistogramWidget.cpp:241:61: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] - 241 | (fontMetrics.width(QString::number(0))) / 2, yPos, boxWidth, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.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/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] @@ -1636,8 +1650,31 @@ LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] 51 | void LowScoringSegParams::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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.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] + 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"); + | ^~~~~~~~~~~~~~ +AlignmentParameters.cpp: In member function 'virtual void AlignmentParameters::showEvent(QShowEvent*)': +AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter] + 48 | void AlignmentParameters::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ +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) + | ^ +HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] + 61 | int i, number, nlines; + | ^~~~~~ +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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, @@ -1649,12 +1686,130 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 AlignmentViewerWidget.h:36, + from mainwindow.h:37, + from mainwindow.cpp:98: +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 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] + 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qvarlengtharray.h:52, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qmetatype.h:48, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qobject.h:54, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qabstractanimation.h:43, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/QtCore:6, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from mainwindow.cpp:90: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20: +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); + | ^~~~~~~~ +/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; + | ^~~~~~~~ +In file included from mainwindow.cpp:99: +WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 88 | auto_ptr params; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from mainwindow.cpp:100: +AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 106 | auto_ptr outFileNames; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from mainwindow.cpp:101: +TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 73 | auto_ptr treeFileNames; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +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; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +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) + | ~~~~~~~~~~~~^~~~~ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp +mainwindow.cpp: In member function 'void MainWindow::writeViewer1AsPostscript(int)': +mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] + 1454 | void MainWindow::writeViewer1AsPostscript(int type) + | ~~~~^~~~ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, @@ -1800,89 +1955,20 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 AlignmentViewerWidget.h:36, - from mainwindow.h:37, - from mainwindow.cpp:98: + 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"); | ^~~~~~~~~~~~~~ -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] - 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qvarlengtharray.h:52, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qmetatype.h:48, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qobject.h:54, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qabstractanimation.h:43, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/QtCore:6, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from mainwindow.cpp:90: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20: -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); - | ^~~~~~~~ -/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; - | ^~~~~~~~ +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 */ + | ^~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1896,38 +1982,14 @@ 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 mainwindow.cpp:99: -WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 88 | auto_ptr params; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from mainwindow.cpp:100: -AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 106 | auto_ptr outFileNames; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from mainwindow.cpp:101: -TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 73 | auto_ptr treeFileNames; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -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; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -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) - | ~~~~~~~~~~~~^~~~~ +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; + | ^~ PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 207 | if(res.isLetter() && resNumber.size() > i - data->firstSeq) @@ -1938,6 +2000,10 @@ PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 421 | if(res.isLetter() && resNumber.size() > i) | ~~~~~~~~~~~~~~~~~^~~ +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(); + | ^~~~~~~~~~ PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] 55 | int err; | ^~~ @@ -1947,10 +2013,6 @@ PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] 74 | int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local | ^~~~~~~ -mainwindow.cpp: In member function 'void MainWindow::writeViewer1AsPostscript(int)': -mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] - 1454 | void MainWindow::writeViewer1AsPostscript(int type) - | ~~~~^~~~ PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)': PSPrinter.cpp:587:32: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 587 | if(data->nameHeader.size() > ix) @@ -1959,6 +2021,7 @@ PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 730 | for(i = fr; i <= lr && i < ruler.length(); 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)': PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 789 | for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) @@ -1966,9 +2029,6 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 ClustalQtParams.h:13, @@ -1980,15 +2040,6 @@ 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"); | ^~~~~~~~~~~~~~ -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"); - | ^~~~~~~~~~~~~~ In file included from SaveSeqFile.cpp:26: 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); @@ -2044,14 +2095,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -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/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ @@ -2064,14 +2107,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -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 clustalW/alignment/AlignmentOutput.h:24, @@ -2185,6 +2220,32 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 SeqNameWidget.h:41, + from SeqNameWidget.cpp:59: +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"); + | ^~~~~~~~~~~~~~ +SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)': +SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable] + 375 | QRect redrawRect = event->rect(); + | ^~~~~~~~~~ +SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()': +SeqNameWidget.cpp:443:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] + 443 | int length = fontMetrics.width(QString(name.c_str())); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/aarch64-linux-gnu/qt5/QtGui/QtGui:26, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from SeqNameWidget.cpp:58: +/usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here + 106 | int width(const QString &, int len = -1) const; + | ^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/ObjectiveScore.h:15, from clustalW/alignment/ObjectiveScore.cpp:10: @@ -2194,6 +2255,10 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -2223,8 +2288,16 @@ /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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp +clustalW/fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()': +clustalW/fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 37 | register int i; + | ^ +clustalW/fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 38 | register char c; + | ^ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -2254,16 +2327,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from SeqNameWidget.h:41, - from SeqNameWidget.cpp:59: -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 WritePostscriptFile.cpp:27: 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); @@ -2319,24 +2382,8 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)': -SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable] - 375 | QRect redrawRect = event->rect(); - | ^~~~~~~~~~ -SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()': -SeqNameWidget.cpp:443:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] - 443 | int length = fontMetrics.width(QString(name.c_str())); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/aarch64-linux-gnu/qt5/QtGui/QtGui:26, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from SeqNameWidget.cpp:58: -/usr/include/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.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, @@ -2347,7 +2394,7 @@ clustalW/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"); | ^~~~~~~~~~~~~~ -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp clustalW/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); | ^~~~~~~~ @@ -2374,21 +2421,6 @@ clustalW/fileInput/FileReader.cpp:555:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp -clustalW/fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()': -clustalW/fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 37 | register int i; - | ^ -clustalW/fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 38 | register char c; - | ^ -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.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) @@ -2406,6 +2438,7 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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*)': clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter] 199 | Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) @@ -2423,7 +2456,8 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.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, @@ -2441,7 +2475,12 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.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; @@ -2451,31 +2490,20 @@ /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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.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: -clustalW/general/../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/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.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; + | ~~~~~~~^ +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.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) - | ~~~~~^~~ -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; - | ^ +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp clustalW/general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)': clustalW/general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 53 | register int p; @@ -2488,13 +2516,19 @@ clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] 519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) | ~~~~~~~~^~~~~~~~~~~~~ -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; - | ~~~~~~~^ -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.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, + from clustalW/interface/../Clustal.h:18, + from clustalW/interface/InteractiveMenu.h:15, + from clustalW/interface/InteractiveMenu.cpp:23: +clustalW/interface/../fileInput/../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/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"); + | ^~~~~~~~~~~~~~ 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); @@ -2503,10 +2537,82 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp +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); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from clustalW/interface/../fileInput/FileReader.h:11: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/interface/../Clustal.h:20: +clustalW/interface/../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); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/interface/../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/interface/../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/interface/../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/interface/../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/interface/../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/interface/../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/interface/../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/interface/../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; + | ^~~~~~~~ +clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()': +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/general/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/general/../alignment/Alignment.h:42, + from clustalW/general/Stats.cpp:15: +clustalW/general/../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/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"); + | ^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/Iteration.h:8, @@ -2517,7 +2623,14 @@ 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"); | ^~~~~~~~~~~~~~ -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.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) + | ~~~~~^~~ +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; + | ^ 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, @@ -2530,18 +2643,6 @@ 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/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/interface/../fileInput/../alignment/Alignment.h:42, - from clustalW/interface/../fileInput/FileReader.h:12, - from clustalW/interface/../Clustal.h:18, - from clustalW/interface/InteractiveMenu.h:15, - from clustalW/interface/InteractiveMenu.cpp:23: -clustalW/interface/../fileInput/../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/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"); - | ^~~~~~~~~~~~~~ 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); | ^~~~~~~~ @@ -2654,76 +2755,6 @@ clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] 170 | int count; | ^~~~~ -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); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from clustalW/interface/../fileInput/FileReader.h:11: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/interface/../Clustal.h:20: -clustalW/interface/../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); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/interface/../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/interface/../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/interface/../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/interface/../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/interface/../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/interface/../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/interface/../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/interface/../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; - | ^~~~~~~~ -clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()': -clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] - 41 | catch(bad_alloc) - | ^~~~~~~~~ -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); - | ~~~~~~~^~~~~~~~ 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'); @@ -2737,26 +2768,37 @@ | ~~~~~~^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, - from clustalW/multipleAlign/MyersMillerProfileAlign.h:10, - from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: + from clustalW/multipleAlign/LowScoreSegProfile.h:13, + from clustalW/multipleAlign/LowScoreSegProfile.cpp:9: 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"); | ^~~~~~~~~~~~~~ -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp +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); + | ~~~~~~~^~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/LowScoreSegProfile.h:13, - from clustalW/multipleAlign/LowScoreSegProfile.cpp:9: + from clustalW/multipleAlign/ProfileBase.h:14, + from clustalW/multipleAlign/MSA.h:10, + from clustalW/multipleAlign/MSA.cpp:16: 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/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, clustalw::AlignmentSteps*, int)': +clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] + 340 | int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 + | ^~~~~~~~~~~~~~ +clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::seqsAlignToProfile(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, int, std::string)': +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.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, @@ -2781,18 +2823,20 @@ 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"); | ^~~~~~~~~~~~~~ -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.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, - from clustalW/multipleAlign/MSA.h:10, - from clustalW/multipleAlign/MSA.cpp:16: + from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, + from clustalW/multipleAlign/MyersMillerProfileAlign.h:10, + from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: 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"); | ^~~~~~~~~~~~~~ +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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, @@ -2803,27 +2847,10 @@ 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/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, clustalw::AlignmentSteps*, int)': -clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] - 340 | int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 - | ^~~~~~~~~~~~~~ -clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::seqsAlignToProfile(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, int, std::string)': -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.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: -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.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, @@ -2835,6 +2862,9 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15: 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"); @@ -2842,7 +2872,6 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.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) @@ -2858,24 +2887,18 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp -In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/tree/../alignment/Alignment.h:42, - from clustalW/tree/ClusterTreeOutput.h:11, - from clustalW/tree/ClusterTreeOutput.cpp:9: -clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +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: +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/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTree.h:20, @@ -2908,6 +2931,80 @@ clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] 580 | int rs = 0, rl = 0; | ^~ +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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, + from clustalW/tree/ClusterTreeOutput.h:11, + from clustalW/tree/ClusterTreeOutput.cpp:9: +clustalW/tree/../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/../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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp +In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/tree/../alignment/Alignment.h:42, + from clustalW/tree/Tree.h:13, + from clustalW/tree/Tree.cpp:10: +clustalW/tree/../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/../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/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); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from clustalW/tree/Tree.h:15: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 278 | auto_ptr Tree::createSets(int firstSeq, int lastSeq) + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/Tree.cpp: In member function 'std::auto_ptr clustalw::Tree::createSets(int, int)': +clustalW/tree/Tree.cpp:280:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 280 | auto_ptr progAlignSteps; + | ^~~~~~~~ +/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp +In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/tree/../alignment/Alignment.h:42, + from clustalW/tree/ClusterTree.h:20, + from clustalW/tree/UnRootedClusterTree.h:8, + from clustalW/tree/UnRootedClusterTree.cpp:9: +clustalW/tree/../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/../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/ClusterTree.h:23: +clustalW/tree/../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; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from clustalW/tree/ClusterTree.h:16: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 70 | auto_ptr quickDistMat; + | ^~~~~~~~ +/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, @@ -2963,16 +3060,64 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/tree/../alignment/Alignment.h:42, - from clustalW/tree/Tree.h:13, - from clustalW/tree/Tree.cpp:10: -clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +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, + from clustalW/tree/UPGMA/RootedClusterTree.h:8, + from clustalW/tree/UPGMA/RootedClusterTree.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/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +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; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from clustalW/tree/UPGMA/../ClusterTree.h:16: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/UPGMA/../ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 70 | auto_ptr quickDistMat; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11: +clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 23 | auto_ptr generateTree(RootedGuideTree* phyTree, + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 51 | auto_ptr progSteps; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 17 | auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/UPGMA/RootedClusterTree.cpp: In member function 'std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)': +clustalW/tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 21 | auto_ptr progSteps; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/TreeInterface.cpp:17: @@ -2988,14 +3133,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -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); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from clustalW/tree/Tree.h:15: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:18: 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); @@ -3016,19 +3153,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -clustalW/tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 278 | auto_ptr Tree::createSets(int firstSeq, int lastSeq) - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/tree/Tree.cpp: In member function 'std::auto_ptr clustalw::Tree::createSets(int, int)': -clustalW/tree/Tree.cpp:280:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 280 | auto_ptr progAlignSteps; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ clustalW/tree/TreeInterface.cpp:103:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 103 | auto_ptr | ^~~~~~~~ @@ -3104,7 +3228,6 @@ /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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.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, @@ -3115,96 +3238,19 @@ 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"); | ^~~~~~~~~~~~~~ -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; - | ^ -In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/tree/../alignment/Alignment.h:42, - from clustalW/tree/ClusterTree.h:20, - from clustalW/tree/UnRootedClusterTree.h:8, - from clustalW/tree/UnRootedClusterTree.cpp:9: -clustalW/tree/../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/../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/ClusterTree.h:23: -clustalW/tree/../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; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from clustalW/tree/ClusterTree.h:16: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 70 | auto_ptr quickDistMat; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -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, - from clustalW/tree/UPGMA/RootedClusterTree.h:8, - from clustalW/tree/UPGMA/RootedClusterTree.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"); - | ^~~~~~~~~~~~~~ -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; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from clustalW/tree/UPGMA/../ClusterTree.h:16: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/tree/UPGMA/../ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 70 | auto_ptr quickDistMat; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, - | ^~~~~~~~ -/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -dM -E -o moc_predefs.h /usr/lib/aarch64-linux-gnu/qt5/mkspecs/features/data/dummy.cpp -In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11: -clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 23 | auto_ptr generateTree(RootedGuideTree* phyTree, - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 51 | auto_ptr progSteps; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 17 | auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -clustalW/tree/UPGMA/RootedClusterTree.cpp: In member function 'std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)': -clustalW/tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 21 | auto_ptr progSteps; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ +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); + | ^ +clustalW/substitutionMatrix/SubMatrix.cpp:998:9: note: 'n' was declared here + 998 | int n, llimit, ulimit; + | ^ /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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.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, @@ -3216,11 +3262,19 @@ 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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include HistogramWidget.h -o moc_HistogramWidget.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include LowScoringSegParams.h -o moc_LowScoringSegParams.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include mainwindow.h -o moc_mainwindow.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include ProteinGapParameters.h -o moc_ProteinGapParameters.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include PSPrinter.h -o moc_PSPrinter.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.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, @@ -3232,14 +3286,9 @@ 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"); | ^~~~~~~~~~~~~~ -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); - | ^ -clustalW/substitutionMatrix/SubMatrix.cpp:998:9: note: 'n' was declared here - 998 | int n, llimit, ulimit; - | ^ -/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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include SearchForString.h -o moc_SearchForString.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include SecStructOptions.h -o moc_SecStructOptions.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include SeqNameWidget.h -o moc_SeqNameWidget.cpp clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ @@ -3260,19 +3309,6 @@ /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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include HistogramWidget.h -o moc_HistogramWidget.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include LowScoringSegParams.h -o moc_LowScoringSegParams.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include mainwindow.h -o moc_mainwindow.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include ProteinGapParameters.h -o moc_ProteinGapParameters.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include PSPrinter.h -o moc_PSPrinter.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include SearchForString.h -o moc_SearchForString.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include SecStructOptions.h -o moc_SecStructOptions.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include SeqNameWidget.h -o moc_SeqNameWidget.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include TreeFormatOptions.h -o moc_TreeFormatOptions.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include TreeOutputFileNames.h -o moc_TreeOutputFileNames.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/aarch64-linux-gnu/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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/14 -I/usr/include/aarch64-linux-gnu/c++/14 -I/usr/include/c++/14/backward -I/usr/lib/gcc/aarch64-linux-gnu/14/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include WritePostscriptFile.h -o moc_WritePostscriptFile.cpp @@ -3299,6 +3335,7 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3318,6 +3355,18 @@ /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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from HelpDisplayWidget.h:18, + from moc_HelpDisplayWidget.cpp:10: +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 clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3347,40 +3396,13 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from HelpDisplayWidget.h:18, - from moc_HelpDisplayWidget.cpp:10: -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from ColorFileXmlParser.h:9, - from moc_ColorFileXmlParser.cpp:10: -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/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 AlignmentViewerWidget.h:36, @@ -3392,30 +3414,7 @@ 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 clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from PSPrinter.h:11, - from moc_PSPrinter.cpp:10: -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 clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from SaveSeqFile.h:9, - from moc_SaveSeqFile.cpp:10: -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.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] @@ -3484,6 +3483,53 @@ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, + from HardCodedColorScheme.h:8, + from ColorParameters.h:11, + from ColorFileXmlParser.h:9, + from moc_ColorFileXmlParser.cpp:10: +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 clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from HardCodedColorScheme.h:8, + from ColorParameters.h:11, + from PSPrinter.h:11, + from moc_PSPrinter.cpp:10: +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 clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from SeqNameWidget.h:41, + from moc_SeqNameWidget.cpp:10: +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 clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from SaveSeqFile.h:9, + from moc_SaveSeqFile.cpp:10: +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 clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, from TreeOutputFileNames.h:10, from moc_TreeOutputFileNames.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -3519,16 +3565,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from SeqNameWidget.h:41, - from moc_SeqNameWidget.cpp:10: -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++ -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o /usr/lib/aarch64-linux-gnu/libQt5Widgets.so /usr/lib/aarch64-linux-gnu/libQt5Gui.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so /usr/lib/aarch64-linux-gnu/libQt5Core.so -lGL -lpthread /usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./clustalW/multipleAlign/Iteration.cpp:231:(.text+0x10b8): warning: the use of `tmpnam' is dangerous, better use `mkstemp' @@ -3563,8 +3599,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-9_arm64.deb'. dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-9_arm64.deb'. +dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-9_arm64.deb'. dpkg-genbuildinfo --build=binary -O../clustalx_2.1+lgpl-9_arm64.buildinfo dpkg-genchanges --build=binary -O../clustalx_2.1+lgpl-9_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3572,12 +3608,14 @@ 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/1591934/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1591934/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/1057078 and its subdirectories -I: Current time: Sun Feb 2 23:53:59 -12 2025 -I: pbuilder-time-stamp: 1738583639 +I: removing directory /srv/workspace/pbuilder/1591934 and its subdirectories +I: Current time: Mon Mar 9 08:18:26 +14 2026 +I: pbuilder-time-stamp: 1772993906