Diff of the two buildlogs: -- --- b1/build.log 2023-05-12 15:13:11.054852569 +0000 +++ b2/build.log 2023-05-12 15:26:07.600855524 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 13 09:27:12 -12 2024 -I: pbuilder-time-stamp: 1718314032 +I: Current time: Sat May 13 05:13:16 +14 2023 +I: pbuilder-time-stamp: 1683904396 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./clustalx_2.1+lgpl.orig.tar.gz] I: copying [./clustalx_2.1+lgpl-9.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Dec 4 10:20:42 2020 -12 +gpgv: Signature made Sat Dec 5 12:20:42 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -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/21298/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13551/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-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 May 13 05:13 /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/13551/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13551/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='21298' - PS1='# ' - PS2='> ' + 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=13551 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.my3e2W41/pbuilderrc_ZK8N --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.my3e2W41/b1 --logfile b1/build.log clustalx_2.1+lgpl-9.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.my3e2W41/pbuilderrc_DUuE --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.my3e2W41/b2 --logfile b2/build.log --extrapackages usrmerge clustalx_2.1+lgpl-9.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink9-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 13 04:49 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/21298/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/13551/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -305,7 +337,7 @@ Get: 186 http://deb.debian.org/debian bookworm/main arm64 qtbase5-dev-tools arm64 5.15.8+dfsg-7 [706 kB] Get: 187 http://deb.debian.org/debian bookworm/main arm64 qtbase5-dev arm64 5.15.8+dfsg-7 [1117 kB] Get: 188 http://deb.debian.org/debian bookworm/main arm64 qttools5-dev-tools arm64 5.15.8-2 [1001 kB] -Fetched 136 MB in 4s (38.0 MB/s) +Fetched 136 MB in 3s (47.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libglib2.0-0: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 ... 19616 files and directories currently installed.) @@ -1078,8 +1110,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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/13551/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/13551/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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 @@ -1173,6 +1214,28 @@ 251 | if(colorNum > 0 && colorNum - 1 < colorPar.size()) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 ColumnScoreParams.o ColumnScoreParams.cpp +In file included from clustalW/substitutionMatrix/globalmatrix.h:8, + from AlignmentParameters.cpp:22: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +AlignmentParameters.cpp: In member function 'virtual void AlignmentParameters::showEvent(QShowEvent*)': +AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter] + 48 | void AlignmentParameters::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ +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 clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1202,41 +1265,6 @@ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, - from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from ColorFileXmlParser.h:9, - from ColorFileXmlParser.cpp:3: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)': -ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] - 85 | QTreeWidgetItem *parentItem) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ -ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)': -ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] - 138 | void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ -ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)': -ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] - 175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from 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 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] @@ -1245,16 +1273,6 @@ 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 AlignmentWidget.h:41, - from AlignmentWidget.cpp:49: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -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; | ^~~~~~~~ @@ -1318,6 +1336,16 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from AlignmentWidget.h:41, + from AlignmentWidget.cpp:49: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ @@ -1336,16 +1364,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)': -AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder] - 170 | bool blackAndWhite; - | ^~~~~~~~~~~~~ -AlignmentWidget.h:161:27: warning: 'std::vector >* AlignmentWidget::selectedColoredRes' [-Wreorder] - 161 | std::vector* selectedColoredRes; - | ^~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] - 65 | AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) - | ^~~~~~~~~~~~~~~ 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++) @@ -1357,6 +1375,33 @@ 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 ) + | ~~~~~~~~~~~~~~~^~~~~ +AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)': +AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder] + 170 | bool blackAndWhite; + | ^~~~~~~~~~~~~ +AlignmentWidget.h:161:27: warning: 'std::vector >* AlignmentWidget::selectedColoredRes' [-Wreorder] + 161 | std::vector* selectedColoredRes; + | ^~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] + 65 | AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) + | ^~~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calculatePixMaps()': AlignmentWidget.cpp:225:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 225 | for(unsigned int j = 0; j < lengthLongestSeq; j++) @@ -1373,10 +1418,6 @@ AlignmentWidget.cpp:291:86: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 291 | if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j) | ~~~~~~~~~~~~~~~~~~~~~^~~ -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 ) - | ~~~~~~~~~~~~~~~^~~~~ AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable] 215 | int codeForSpace = clustalw::userParameters->resIndex( | ^~~~~~~~~~~~ @@ -1398,10 +1439,22 @@ AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 569 | if(selectedRes >= selectedColoredRes->size()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] + 85 | QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ +ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] + 138 | void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()': AlignmentWidget.cpp:689:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 689 | for(int j = 1; j <= strongGroup.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~ +ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] + 175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ AlignmentWidget.cpp: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++) | ~~^~~~~~~~~~~~~~~~~~~ @@ -1465,18 +1518,6 @@ /usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ -In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from AlignmentParameters.cpp:22: -clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -AlignmentParameters.cpp: In member function 'virtual void AlignmentParameters::showEvent(QShowEvent*)': -AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter] - 48 | void AlignmentParameters::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 FileDialog.o FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 HardCodedColorScheme.o HardCodedColorScheme.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 HelpDisplayWidget.o HelpDisplayWidget.cpp @@ -1615,13 +1656,6 @@ 64 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 -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; - | ^~~~~~ 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()) @@ -1647,6 +1681,13 @@ /usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ +HelpDisplayWidget.cpp: In member function 'std::string* HelpDisplayWidget::loadHelpInformation(char)': +HelpDisplayWidget.cpp:147:29: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] + 147 | catch(ifstream::failure e) + | ^ +HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] + 61 | int i, number, nlines; + | ^~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 @@ -1843,10 +1884,10 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] 781 | int psX, psY, curveBottom; | ^~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, @@ -2100,6 +2141,7 @@ clustalW/alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 122 | register int sl; /* which have code = gap_pos2 */ | ^~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()': clustalW/alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 617 | register int sl; @@ -2108,6 +2150,7 @@ clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable] 1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin(); | ^~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/Alignment.h:42, from ClustalQtParams.h:13, @@ -2134,8 +2177,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/Alignment.h:42, from clustalW/alignment/AlignmentOutput.h:24, @@ -2146,6 +2187,15 @@ 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/ObjectiveScore.h:15, + from clustalW/alignment/ObjectiveScore.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"); + | ^~~~~~~~~~~~~~ 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); | ^~~~~~~~ @@ -2202,17 +2252,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -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"); - | ^~~~~~~~~~~~~~ clustalW/alignment/AlignmentOutput.cpp:512:40: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 512 | bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) | ^~~~~~~~ @@ -2225,6 +2264,37 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion)': +clustalW/alignment/AlignmentOutput.cpp:673:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] + 673 | catch(VectorOutOfRange e) + | ^ +clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)': +clustalW/alignment/AlignmentOutput.cpp:868:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] + 868 | catch(VectorOutOfRange e) + | ^ +clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)': +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 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/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/../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.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) + | ^ WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 88 | auto_ptr params; | ^~~~~~~~ @@ -2240,21 +2310,20 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion)': -clustalW/alignment/AlignmentOutput.cpp:673:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] - 673 | catch(VectorOutOfRange e) - | ^ -clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)': -clustalW/alignment/AlignmentOutput.cpp:868:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] - 868 | 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::phylipOut(clustalw::Alignment*, clustalw::outputRegion)': -clustalW/alignment/AlignmentOutput.cpp:1027:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] - 1027 | 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: 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: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 WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] @@ -2281,10 +2350,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ @@ -2315,30 +2380,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -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/ObjectiveScore.h:15, - from clustalW/alignment/ObjectiveScore.cpp:10: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 @@ -2355,7 +2396,6 @@ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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, @@ -2381,6 +2421,7 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp clustalW/fileInput/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) @@ -2396,6 +2437,19 @@ clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter] 34 | vector MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) | ~~~~~~~~^~~~~~~~~~~~ +clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual void clustalw::MSFFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': +clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] + 246 | void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] + 246 | void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter] + 247 | string& secStructName, int &structPenalties, int length) + | ~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter] + 247 | string& secStructName, int &structPenalties, int length) + | ~~~~^~~~~~ 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) @@ -2413,19 +2467,7 @@ clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] 446 | int &structPenalties, int length) | ~~~~^~~~~~ -clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual void clustalw::MSFFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': -clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] - 246 | void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] - 246 | void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter] - 247 | string& secStructName, int &structPenalties, int length) - | ~~~~~~~~^~~~~~~~~~~~~ -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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 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, @@ -2439,18 +2481,13 @@ 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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 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; @@ -2464,8 +2501,10 @@ 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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp In file included from clustalW/general/OutputFile.cpp:9: clustalW/general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; @@ -2475,6 +2514,7 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/general/../alignment/Alignment.h:42, from clustalW/general/Stats.cpp:15: @@ -2484,12 +2524,13 @@ clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp clustalW/general/UserParameters.cpp: In constructor 'clustalw::UserParameters::UserParameters(bool)': clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter] 33 | UserParameters::UserParameters(bool log) | ~~~~~^~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp clustalW/general/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; @@ -2506,6 +2547,7 @@ clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] 519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) | ~~~~~~~~^~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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); @@ -2514,19 +2556,19 @@ clustalW/general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/interface/../fileInput/../alignment/Alignment.h:42, from clustalW/interface/../fileInput/FileReader.h:12, from clustalW/interface/../Clustal.h:18, - from clustalW/interface/InteractiveMenu.h:15, - from clustalW/interface/InteractiveMenu.cpp:23: + from clustalW/interface/CommandLineParser.h:18, + from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/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); | ^~~~~~~~ @@ -2590,159 +2632,143 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()': -clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] - 41 | catch(bad_alloc) - | ^~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 +In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/multipleAlign/../alignment/Alignment.h:42, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~ In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/interface/../fileInput/../alignment/Alignment.h:42, from clustalW/interface/../fileInput/FileReader.h:12, from clustalW/interface/../Clustal.h:18, - from clustalW/interface/CommandLineParser.h:18, - from clustalW/interface/CommandLineParser.cpp:13: + from clustalW/interface/InteractiveMenu.h:15, + from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); - | ^~~~~~~~ +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, + | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, - from clustalW/interface/../fileInput/FileReader.h:11: + from clustalW/multipleAlign/../tree/TreeInterface.h:17: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from clustalW/interface/../Clustal.h:20: -clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); - | ^~~~~~~~ +clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, + | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, - | ^~~~~~~~ +clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, + | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 75 | auto_ptr clustalOutFile; +clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 76 | auto_ptr gcgOutFile; +clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 77 | auto_ptr nbrfOutFile; +clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 78 | auto_ptr phylipOutFile; +clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 79 | auto_ptr gdeOutFile; - | ^~~~~~~~ +clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); + | ^~~~~~~~ +In file included from /usr/include/c++/12/memory:76, + from clustalW/interface/../fileInput/FileReader.h:11: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 80 | auto_ptr nexusOutFile; - | ^~~~~~~~ +In file included from clustalW/interface/../Clustal.h:20: +clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); + | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 81 | auto_ptr fastaOutFile; - | ^~~~~~~~ +clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, + | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -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/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 -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, +clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 75 | auto_ptr clustalOutFile; | ^~~~~~~~ -In file included from /usr/include/c++/12/memory:76, - from clustalW/multipleAlign/../tree/TreeInterface.h:17: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, +clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, +clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, +clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, +clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, +clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, +clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; @@ -2751,7 +2777,10 @@ 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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()': +clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] + 41 | catch(bad_alloc) + | ^~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, @@ -2763,9 +2792,6 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 231 | tmpnam (buffer); - | ~~~~~~~^~~~~~~~ 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 @@ -2774,6 +2800,7 @@ clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] 359 | string phylipName) | ~~~~~~~^~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, @@ -2785,7 +2812,20 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 231 | tmpnam (buffer); + | ~~~~~~~^~~~~~~~ +clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()': +clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] + 520 | clustalObj->getHelp('C'); + | ~~~~~~~~~~~~~~~~~~~^~~~~ +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/ProfileBase.h:14, @@ -2793,6 +2833,7 @@ 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"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/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"); | ^~~~~~~~~~~~~~ @@ -2837,13 +2878,7 @@ 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 -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"); - | ^~~~~~~~~~~~~~ -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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, @@ -2855,6 +2890,13 @@ 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/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"); + | ^~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::tempInterface(int, int)': clustalW/substitutionMatrix/SubMatrix.cpp:1613:35: warning: unused parameter 'alignResidueType' [-Wunused-parameter] 1613 | void SubMatrix::tempInterface(int alignResidueType, int alignType) @@ -2870,10 +2912,8 @@ clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] 1717 | int maxRes; | ^~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTree.h:20, @@ -2906,6 +2946,8 @@ clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] 580 | int rs = 0, rl = 0; | ^~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTreeOutput.h:11, @@ -2916,7 +2958,6 @@ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 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; @@ -2931,6 +2972,27 @@ 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++/12/memory:76, + from clustalW/tree/Tree.h:15: +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | 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++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | 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++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, @@ -2986,27 +3048,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -clustalW/tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 26 | auto_ptr createSets(int firstSeq, int lastSeq); - | ^~~~~~~~ -In file included from /usr/include/c++/12/memory:76, - from clustalW/tree/Tree.h:15: -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | 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++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | 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++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/TreeInterface.cpp:17: @@ -3143,6 +3184,9 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/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); @@ -3150,13 +3194,9 @@ clustalW/substitutionMatrix/SubMatrix.cpp:998:9: note: 'n' was declared here 998 | int n, llimit, ulimit; | ^ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, @@ -3167,12 +3207,11 @@ 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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, - from clustalW/tree/UPGMA/RootedGuideTree.h:17, - from clustalW/tree/UPGMA/RootedTreeOutput.h:15, - from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: + 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"); | ^~~~~~~~~~~~~~ @@ -3181,9 +3220,9 @@ | ^~~~~~~~~~~~~~ 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: + from clustalW/tree/UPGMA/RootedGuideTree.h:17, + from clustalW/tree/UPGMA/RootedTreeOutput.h:15, + from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ @@ -3205,8 +3244,7 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp 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, | ^~~~~~~~ @@ -3239,6 +3277,11 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.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, @@ -3250,10 +3293,10 @@ 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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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, | ^~~~~~~~ @@ -3274,8 +3317,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/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/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/aarch64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/aarch64-linux-gnu/12/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.cpp @@ -3306,24 +3347,22 @@ 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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 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 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"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 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 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"); | ^~~~~~~~~~~~~~ @@ -3338,27 +3377,28 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -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++/12/memory:76, - from moc_BootstrapTreeDialog.cpp:9: -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 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 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"); | ^~~~~~~~~~~~~~ +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++/12/memory:76, + from moc_BootstrapTreeDialog.cpp:9: +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -3372,6 +3412,7 @@ 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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 @@ -3387,6 +3428,8 @@ 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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, @@ -3398,9 +3441,8 @@ 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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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 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] @@ -3466,7 +3508,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/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, @@ -3506,38 +3547,38 @@ 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: + 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] 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; +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++/12/memory:76, - from moc_WritePostscriptFile.cpp:9: + from moc_TreeOutputFileNames.cpp:9: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ 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: + from WritePostscriptFile.h:10, + from moc_WritePostscriptFile.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"); | ^~~~~~~~~~~~~~ -TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 73 | auto_ptr treeFileNames; +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++/12/memory:76, - from moc_TreeOutputFileNames.cpp:9: + from moc_WritePostscriptFile.cpp:9: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ @@ -3571,8 +3612,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-9_arm64.deb'. dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-9_arm64.deb'. +dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-9_arm64.deb'. dpkg-genbuildinfo --build=binary -O../clustalx_2.1+lgpl-9_arm64.buildinfo dpkg-genchanges --build=binary -O../clustalx_2.1+lgpl-9_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3580,12 +3621,14 @@ 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/13551/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13551/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/21298 and its subdirectories -I: Current time: Thu Jun 13 09:36:09 -12 2024 -I: pbuilder-time-stamp: 1718314569 +I: removing directory /srv/workspace/pbuilder/13551 and its subdirectories +I: Current time: Sat May 13 05:26:06 +14 2023 +I: pbuilder-time-stamp: 1683905166