Diff of the two buildlogs: -- --- b1/build.log 2024-05-28 18:34:51.010455877 +0000 +++ b2/build.log 2024-05-28 18:36:27.026372145 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 30 12:56:27 -12 2025 -I: pbuilder-time-stamp: 1751331387 +I: Current time: Tue Jul 1 14:57:52 +14 2025 +I: pbuilder-time-stamp: 1751331472 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying qt5.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/970553/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1122636/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Jul 1 00:58 /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/1122636/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1122636/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='ff41685e9f9a4425a57778653d82ae13' - 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='970553' - PS1='# ' - PS2='> ' + INVOCATION_ID=8b594a7b238b48259596ba65eeeee0b3 + 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=1122636 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.HLp3ekAG/pbuilderrc_7XFC --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HLp3ekAG/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.HLp3ekAG/pbuilderrc_Y6mZ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HLp3ekAG/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 codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 29 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/970553/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1122636/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -313,7 +345,7 @@ Get: 194 http://deb.debian.org/debian unstable/main arm64 qtbase5-dev-tools arm64 5.15.13+dfsg-2 [717 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 qtbase5-dev arm64 5.15.13+dfsg-2 [1119 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 qttools5-dev-tools arm64 5.15.13-3 [1004 kB] -Fetched 142 MB in 1s (222 MB/s) +Fetched 142 MB in 1s (206 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libglib2.0-0t64: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 ... 19762 files and directories currently installed.) @@ -950,8 +982,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jul 1 00:56:59 UTC 2025. -Universal Time is now: Tue Jul 1 00:56:59 UTC 2025. +Local time is now: Tue Jul 1 00:58:25 UTC 2025. +Universal Time is now: Tue Jul 1 00:58:25 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libcap2-bin (1:2.66-5) ... @@ -1129,7 +1161,11 @@ 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/1122636/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1122636/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 @@ -1180,6 +1216,29 @@ from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, + 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"); + | ^~~~~~~~~~~~~~ +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 HelpDisplayWidget.h:18, + from HelpDisplayWidget.cpp:15: +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 HistogramWidget.o HistogramWidget.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 ColorParameters.cpp:1: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -1226,43 +1285,205 @@ ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 251 | if(colorNum > 0 && colorNum - 1 < colorPar.size()) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 +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 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, from HardCodedColorScheme.h:8, - from HardCodedColorScheme.cpp:1: + 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"); | ^~~~~~~~~~~~~~ -g++ -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 +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) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ +g++ -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 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 HelpDisplayWidget.cpp:15: + 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"); | ^~~~~~~~~~~~~~ -g++ -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 +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++/13/memory:78, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': +AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 588 | for(i = 0; i < len && i < gapMask->size(); i++) + | ~~^~~~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': +AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 645 | for (i = 0; i < len && i < _secStructMask->size();i++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 652 | for(i = 0; i < len && i < ssMask.size(); i++) + | ~~^~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)': +AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] + 781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) + | ~~~~~~~~~~~~~~~^~~~~ In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from AlignmentParameters.cpp:22: + from ColumnScoreParams.cpp:23: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)': +ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] + 51 | void ColumnScoreParams::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from BootstrapTreeDialog.h:11, + from BootstrapTreeDialog.cpp:18: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +g++ -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 +BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 70 | auto_ptr treeFileNames; + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + 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 BootstrapTreeDialog.cpp:8: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +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"); | ^~~~~~~~~~~~~~ -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) - | ~~~~~~~~~~~~^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, @@ -1321,7 +1542,7 @@ 569 | if(selectedRes >= selectedColoredRes->size()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from ColumnScoreParams.cpp:23: + 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"); | ^~~~~~~~~~~~~~ @@ -1332,6 +1553,10 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~ +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:693:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 693 | for(int j = 1; j <= weakGroup.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~ @@ -1344,10 +1569,6 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~ -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) - | ~~~~~~~~~~~~^~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~ @@ -1365,16 +1586,6 @@ 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)) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from AlignmentViewerWidget.h:36, - from AlignmentViewerWidget.cpp:66: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()': AlignmentWidget.cpp:1039:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1039 | for(int j = 0; j < aminoAcid.size(); j++) @@ -1409,21 +1620,29 @@ /usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); - | ^~~~~~~~ +In file included from clustalW/Clustal.h:18, + from mainwindow.h:45, + from main.cpp:24: +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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: + from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/aarch64-linux-gnu/qt5/QtGui/qbrush.h:52, + from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpalette.h:46, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:48, + from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QWidget:1, + from QTUtility.h:10, + from main.cpp:22: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ @@ -1475,107 +1694,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': -AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 588 | for(i = 0; i < len && i < gapMask->size(); i++) - | ~~^~~~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': -AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 645 | for (i = 0; i < len && i < _secStructMask->size();i++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 652 | for(i = 0; i < len && i < ssMask.size(); i++) - | ~~^~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)': -AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] - 781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) - | ~~~~~~~~~~~~~~~^~~~~ -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++/13/memory:78, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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 main.o main.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from BootstrapTreeDialog.h:11, - from BootstrapTreeDialog.cpp:18: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 70 | auto_ptr treeFileNames; - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - 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 BootstrapTreeDialog.cpp:8: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -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 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) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ -g++ -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 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()) @@ -1601,94 +1719,23 @@ /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 PairwiseParams.o PairwiseParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -In file included from main.cpp:21: +g++ -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 +In file included from clustalW/substitutionMatrix/globalmatrix.h:8, + from LowScoringSegParams.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -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 +LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': +LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] + 51 | void LowScoringSegParams::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ g++ -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/Clustal.h:18, - from mainwindow.h:45, - from main.cpp:24: -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++/13/memory:78, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - 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/qbrush.h:52, - from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpalette.h:46, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:48, - from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QWidget:1, - from QTUtility.h:10, - from main.cpp:22: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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 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 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1700,19 +1747,8 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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/substitutionMatrix/globalmatrix.h:8, - from LowScoringSegParams.cpp:22: -clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': -LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] - 51 | void LowScoringSegParams::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ g++ -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 @@ -1729,6 +1765,7 @@ 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"); | ^~~~~~~~~~~~~~ +g++ -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 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] @@ -1851,7 +1888,6 @@ 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 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, from clustalW/fileInput/../alignment/Alignment.h:42, @@ -1987,52 +2023,56 @@ g++ -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 ClustalQtParams.h:13, - from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from PSPrinter.h:11, - from PSPrinter.cpp:20: + 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"); | ^~~~~~~~~~~~~~ -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) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 307 | if(res.isLetter() && resNumber.size() > seq) - | ~~~~~~~~~~~~~~~~~^~~~~ -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) - | ~~~~~~~~~~~~~~~~~^~~ -PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] - 55 | int err; - | ^~~ -PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] - 73 | int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local - | ^~~~~~~ -PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] - 74 | int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local - | ^~~~~~~ -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) - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +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 AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp -PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': -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++) - | ~~^~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] - 781 | int psX, psY, curveBottom; - | ^~~ +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 TreeOutputFileNames.cpp:17: +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"); + | ^~~~~~~~~~~~~~ +TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 73 | auto_ptr treeFileNames; + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + 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 TreeOutputFileNames.cpp:7: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from clustalW/alignment/Alignment.cpp:25: @@ -2068,17 +2108,6 @@ 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 ClustalQtParams.h:13, - from SaveSeqFile.h:9, - from SaveSeqFile.cpp:23: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ clustalW/alignment/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); | ^~~~~~~~ @@ -2159,10 +2188,43 @@ clustalW/alignment/AlignmentOutput.cpp:1027:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 1027 | catch(VectorOutOfRange e) | ^ -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); - | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)': +clustalW/alignment/AlignmentOutput.cpp:1156:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] + 1156 | catch(VectorOutOfRange e) + | ^ +clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)': +clustalW/alignment/AlignmentOutput.cpp:1445:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] + 1445 | catch(VectorOutOfRange e) + | ^ +clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)': +clustalW/alignment/AlignmentOutput.cpp:1560:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] + 1560 | catch(VectorOutOfRange e) + | ^ +clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion)': +clustalW/alignment/AlignmentOutput.cpp:2095:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] + 2095 | catch(VectorOutOfRange e) + | ^ +clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] + 2102 | catch(exception e) + | ^ +clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)': +clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] + 2351 | catch(VectorOutOfRange e) + | ^ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from WritePostscriptFile.h:10, + from WritePostscriptFile.cpp:24: +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"); + | ^~~~~~~~~~~~~~ +WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 88 | auto_ptr params; + | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, @@ -2171,7 +2233,14 @@ 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 SaveSeqFile.cpp:14: + from WritePostscriptFile.cpp:14: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +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); + | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ @@ -2199,10 +2268,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)': -clustalW/alignment/AlignmentOutput.cpp:1156:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] - 1156 | catch(VectorOutOfRange e) - | ^ 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; | ^~~~~~~~ @@ -2227,51 +2292,55 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)': -clustalW/alignment/AlignmentOutput.cpp:1445:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] - 1445 | catch(VectorOutOfRange e) - | ^ -clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)': -clustalW/alignment/AlignmentOutput.cpp:1560:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] - 1560 | catch(VectorOutOfRange e) - | ^ -clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion)': -clustalW/alignment/AlignmentOutput.cpp:2095:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] - 2095 | catch(VectorOutOfRange e) - | ^ -clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] - 2102 | catch(exception e) - | ^ -clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)': -clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] - 2351 | catch(VectorOutOfRange e) - | ^ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from SeqNameWidget.h:41, - from SeqNameWidget.cpp:59: + from ClustalQtParams.h:13, + from HardCodedColorScheme.h:8, + from ColorParameters.h:11, + from PSPrinter.h:11, + from PSPrinter.cpp:20: 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; - | ^~~~~ +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) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 307 | if(res.isLetter() && resNumber.size() > seq) + | ~~~~~~~~~~~~~~~~~^~~~~ +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) + | ~~~~~~~~~~~~~~~~~^~~ +PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] + 55 | int err; + | ^~~ +PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] + 73 | int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local + | ^~~~~~~ +PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] + 74 | int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local + | ^~~~~~~ +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) + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ g++ -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 +PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': +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++) + | ~~^~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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 Sequence.o clustalW/alignment/Sequence.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/ObjectiveScore.h:15, from clustalW/alignment/ObjectiveScore.cpp:10: @@ -2281,99 +2350,22 @@ 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 -g++ -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 -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 InFileStream.o clustalW/fileInput/InFileStream.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, - from clustalW/fileInput/FileReader.cpp:29: -clustalW/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/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 MSFFileParser.o clustalW/fileInput/MSFFileParser.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); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from clustalW/fileInput/FileReader.h:11: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -clustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)': -clustalW/fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 155 | auto_ptr fileParser; // Means we dont need to delete it! - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -clustalW/fileInput/FileReader.cpp: At global scope: -clustalW/fileInput/FileReader.cpp:426:42: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 426 | void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -clustalW/fileInput/FileReader.cpp: In member function 'void clustalw::FileReader::checkInfile(int*, std::auto_ptr&)': -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 PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp -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 TreeOutputFileNames.cpp:17: -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"); - | ^~~~~~~~~~~~~~ -TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 73 | auto_ptr treeFileNames; - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - 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 TreeOutputFileNames.cpp:7: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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 PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, - from WritePostscriptFile.h:10, - from WritePostscriptFile.cpp:24: + from SaveSeqFile.h:9, + from SaveSeqFile.cpp:23: 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"); | ^~~~~~~~~~~~~~ -WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 88 | auto_ptr params; - | ^~~~~~~~ +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); + | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, @@ -2382,15 +2374,7 @@ 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 WritePostscriptFile.cpp:14: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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 RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp -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); - | ^~~~~~~~ + from SaveSeqFile.cpp:14: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ @@ -2442,6 +2426,85 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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 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 +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 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 +g++ -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 +In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/fileInput/../alignment/Alignment.h:42, + from clustalW/fileInput/FileReader.h:12, + from clustalW/fileInput/FileReader.cpp:29: +clustalW/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/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/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++/13/memory:78, + from clustalW/fileInput/FileReader.h:11: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +clustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)': +clustalW/fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 155 | auto_ptr fileParser; // Means we dont need to delete it! + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +clustalW/fileInput/FileReader.cpp: At global scope: +clustalW/fileInput/FileReader.cpp:426:42: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 426 | void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +clustalW/fileInput/FileReader.cpp: In member function 'void clustalw::FileReader::checkInfile(int*, std::auto_ptr&)': +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 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/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) + | ~~~~~~~~^~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': +clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] + 444 | void PearsonFileParser::getSecStructure(vector& gapPenaltyMask, + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter] + 445 | vector& secStructMask, string& secStructName, + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter] + 445 | vector& secStructMask, string& secStructName, + | ~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] + 446 | int &structPenalties, int length) + | ~~~~^~~~~~ +clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': +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 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 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) @@ -2459,8 +2522,7 @@ 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 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 Utility.o clustalW/general/Utility.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, @@ -2474,30 +2536,6 @@ clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter] 293 | 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 OutputFile.o clustalW/general/OutputFile.cpp -clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': -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 Stats.o clustalW/general/Stats.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) - | ~~~~~~~~^~~~~~~~~~~~ -clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': -clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] - 444 | void PearsonFileParser::getSecStructure(vector& gapPenaltyMask, - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter] - 445 | vector& secStructMask, string& secStructName, - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter] - 445 | vector& secStructMask, string& secStructName, - | ~~~~~~~~^~~~~~~~~~~~~ -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 SymMatrix.o clustalW/general/SymMatrix.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; @@ -2511,8 +2549,6 @@ clustalW/general/ClustalWResources.cpp:104:10: note: destination object 'delim' of size 1 104 | 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 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 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; @@ -2524,50 +2560,18 @@ | ^~~~~~~~ g++ -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 g++ -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 -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; - | ^ -clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)': -clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable] - 251 | int n; - | ^ 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/Utility.cpp: In member function 'virtual void clustalw::Utility::setInfoLabelPtr(QLabel*)': -clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] - 519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) - | ~~~~~~~~^~~~~~~~~~~~~ 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 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 g++ -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/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -clustalW/general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)': -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -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 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 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, @@ -2580,6 +2584,7 @@ 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"); | ^~~~~~~~~~~~~~ +g++ -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 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); | ^~~~~~~~ @@ -2643,6 +2648,29 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +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 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 +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; + | ^ +clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)': +clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable] + 251 | int n; + | ^ +clustalW/general/Utility.cpp: In member function 'virtual void clustalw::Utility::setInfoLabelPtr(QLabel*)': +clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] + 519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) + | ~~~~~~~~^~~~~~~~~~~~~ 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, @@ -2655,7 +2683,6 @@ 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"); | ^~~~~~~~~~~~~~ -g++ -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); | ^~~~~~~~ @@ -2664,13 +2691,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -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: -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"); - | ^~~~~~~~~~~~~~ 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); @@ -2678,9 +2698,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ clustalW/interface/../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, | ^~~~~~~~ @@ -2743,28 +2760,14 @@ 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"); | ^~~~~~~~~~~~~~ -clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()': -clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] - 520 | clustalObj->getHelp('C'); - | ~~~~~~~~~~~~~~~~~~~^~~~~ -clustalW/interface/InteractiveMenu.cpp:521:13: note: here - 521 | case 'Q': - | ^~~~ -clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': -clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1190 | system(lin1.c_str()); - | ~~~~~~^~~~~~~~~~~~~~ -In file included from clustalW/multipleAlign/../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: -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/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +clustalW/general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)': +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, @@ -2776,6 +2779,25 @@ 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) + | ~~~~~~~^~~~~~~~~~ +clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()': +clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] + 520 | clustalObj->getHelp('C'); + | ~~~~~~~~~~~~~~~~~~~^~~~~ +clustalW/interface/InteractiveMenu.cpp:521:13: note: here + 521 | case 'Q': + | ^~~~ +clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': +clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1190 | system(lin1.c_str()); + | ~~~~~~^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, @@ -2821,19 +2843,33 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -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 FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp +In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/multipleAlign/../alignment/Alignment.h:42, + from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, + 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"); + | ^~~~~~~~~~~~~~ clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] 170 | int count; | ^~~~~ +g++ -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/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 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 g++ -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 clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2841,29 +2877,24 @@ | ~~~~~~~^~~~~~~~ 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/ProfileBase.cpp:9: + from clustalW/multipleAlign/ProfileStandard.h:9, + from clustalW/multipleAlign/ProfileStandard.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"); | ^~~~~~~~~~~~~~ -clustalW/multipleAlign/ProfileBase.cpp: In member function 'void clustalw::ProfileBase::calcResidueSpecificPen(clustalw::SeqArray*, std::vector*)': -clustalW/multipleAlign/ProfileBase.cpp:372:25: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 372 | if ((ix < 0) || (ix > _maxAA)) - | ~~~^~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/ProfileWithSub.h:9, - from clustalW/multipleAlign/ProfileWithSub.cpp:9: + from clustalW/multipleAlign/ProfileBase.h:14, + from clustalW/multipleAlign/ProfileBase.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 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, @@ -2875,6 +2906,11 @@ 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"); | ^~~~~~~~~~~~~~ +clustalW/multipleAlign/ProfileBase.cpp: In member function 'void clustalw::ProfileBase::calcResidueSpecificPen(clustalw::SeqArray*, std::vector*)': +clustalW/multipleAlign/ProfileBase.cpp:372:25: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 372 | if ((ix < 0) || (ix > _maxAA)) + | ~~~^~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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/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"); @@ -2897,21 +2933,8 @@ clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] 1717 | int maxRes; | ^~~~~~ -In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/ProfileStandard.h:9, - from clustalW/multipleAlign/ProfileStandard.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 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 -g++ -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 In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, @@ -2923,9 +2946,70 @@ 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"); | ^~~~~~~~~~~~~~ +In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/multipleAlign/../alignment/Alignment.h:42, + from clustalW/multipleAlign/ProfileWithSub.h:9, + from clustalW/multipleAlign/ProfileWithSub.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 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 +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 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/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"); + | ^~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~ +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++/13/memory:78, + from clustalW/tree/Tree.h:15: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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, from clustalW/tree/ClusterTree.h:20, @@ -2951,8 +3035,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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 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 clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)': clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable] 580 | int rs = 0, rl = 0; @@ -2960,47 +3042,108 @@ clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] 580 | int rs = 0, rl = 0; | ^~ -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++/13/memory:78, + from clustalW/tree/UPGMA/../ClusterTree.h:16: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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; + | ^ 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: + 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"); | ^~~~~~~~~~~~~~ -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 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++/13/memory:78, - from clustalW/tree/Tree.h:15: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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) - | ^~~~~~~~ + from clustalW/tree/ClusterTree.h:16: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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; - | ^~~~~~~~ +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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/RootedGuideTree.h:17, + from clustalW/tree/UPGMA/RootedGuideTree.cpp:10: +clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +g++ -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/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/TreeInterface.h:19, @@ -3055,6 +3198,7 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +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/ClusterTree.h:23, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/TreeInterface.cpp:17: @@ -3165,121 +3309,14 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/RootedGuideTree.h:17, - from clustalW/tree/UPGMA/RootedGuideTree.cpp:10: -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -g++ -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 -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 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 /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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.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++/13/memory:78, - from clustalW/tree/ClusterTree.h:16: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/memory:78, - from clustalW/tree/UPGMA/../ClusterTree.h:16: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp -clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)': -clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized] - 1103 | return (maxRes); - | ^ -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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include ColumnScoreParams.h -o moc_ColumnScoreParams.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, @@ -3291,7 +3328,8 @@ 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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include HelpDisplayWidget.h -o moc_HelpDisplayWidget.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, @@ -3300,12 +3338,6 @@ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include HistogramWidget.h -o moc_HistogramWidget.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, | ^~~~~~~~ @@ -3326,6 +3358,10 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/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++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.cpp @@ -3349,7 +3385,6 @@ g++ -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_FileDialog.o moc_FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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_HistogramWidget.o moc_HistogramWidget.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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_LowScoringSegParams.o moc_LowScoringSegParams.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, @@ -3362,60 +3397,59 @@ | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from BootstrapTreeDialog.h:11, - from moc_BootstrapTreeDialog.cpp:10: + from AlignmentWidget.h:41, + from moc_AlignmentWidget.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"); | ^~~~~~~~~~~~~~ -BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 70 | auto_ptr treeFileNames; - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from moc_BootstrapTreeDialog.cpp:9: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | 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_LowScoringSegParams.o moc_LowScoringSegParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -g++ -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 AlignmentWidget.h:41, - from moc_AlignmentWidget.cpp:10: + from ClustalQtParams.h:13, + from AlignOutputFileNames.h:10, + from moc_AlignOutputFileNames.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"); | ^~~~~~~~~~~~~~ +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++/13/memory:78, + from moc_AlignOutputFileNames.cpp:9: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | 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_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 AlignOutputFileNames.h:10, - from moc_AlignOutputFileNames.cpp:10: + from BootstrapTreeDialog.h:11, + from moc_BootstrapTreeDialog.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"); | ^~~~~~~~~~~~~~ -AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 106 | auto_ptr outFileNames; +BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 70 | auto_ptr treeFileNames; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, - from moc_AlignOutputFileNames.cpp:9: + from moc_BootstrapTreeDialog.cpp:9: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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 g++ -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 g++ -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 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3427,7 +3461,10 @@ 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 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 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3441,10 +3478,22 @@ 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_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 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 AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:10: @@ -3457,10 +3506,18 @@ 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: + 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 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"); | ^~~~~~~~~~~~~~ @@ -3535,17 +3592,6 @@ 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] @@ -3564,16 +3610,6 @@ | ^~~~~~~~ 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 WritePostscriptFile.h:10, from moc_WritePostscriptFile.cpp:10: @@ -3630,12 +3666,14 @@ 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/1122636/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1122636/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/970553 and its subdirectories -I: Current time: Mon Jun 30 12:57:47 -12 2025 -I: pbuilder-time-stamp: 1751331467 +I: removing directory /srv/workspace/pbuilder/1122636 and its subdirectories +I: Current time: Tue Jul 1 14:59:23 +14 2025 +I: pbuilder-time-stamp: 1751331563