Diff of the two buildlogs: -- --- b1/build.log 2023-04-22 04:59:57.578374394 +0000 +++ b2/build.log 2023-04-22 05:02:25.523815379 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 21 16:58:18 -12 2023 -I: pbuilder-time-stamp: 1682139498 +I: Current time: Sat May 25 01:23:00 +14 2024 +I: pbuilder-time-stamp: 1716549780 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 [./clustalw_2.1+lgpl.orig.tar.gz] I: copying [./clustalw_2.1+lgpl-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Nov 15 20:43:21 2020 -12 +gpgv: Signature made Mon Nov 16 22:43:21 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,52 +28,84 @@ dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18533/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/7856/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-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 25 01:23 /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/7856/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/7856/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='18533' - 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=7856 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.q4dhrcI9/pbuilderrc_fTcm --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.q4dhrcI9/b1 --logfile b1/build.log clustalw_2.1+lgpl-7.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.q4dhrcI9/pbuilderrc_f5Dz --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.q4dhrcI9/b2 --logfile b2/build.log --extrapackages usrmerge clustalw_2.1+lgpl-7.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 codethink12-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 20 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/18533/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 23 06:50 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/7856/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -139,7 +171,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] -Fetched 18.3 MB in 0s (45.9 MB/s) +Fetched 18.3 MB in 0s (45.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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.) @@ -273,8 +305,17 @@ 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/clustalw-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 > ../clustalw_2.1+lgpl-7_source.changes +I: user script /srv/workspace/pbuilder/7856/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/7856/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/clustalw-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 > ../clustalw_2.1+lgpl-7_source.changes dpkg-buildpackage: info: source package clustalw dpkg-buildpackage: info: source version 2.1+lgpl-7 dpkg-buildpackage: info: source distribution unstable @@ -505,6 +546,7 @@ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, @@ -548,13 +590,14 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp ./fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()': ./fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 37 | register int i; @@ -562,7 +605,6 @@ ./fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 38 | register char c; | ^ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, @@ -574,27 +616,6 @@ ./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"); | ^~~~~~~~~~~~~~ -./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, - | ^~~~~~~~ -In file included from /usr/include/c++/12/memory:76, - from ./tree/UPGMA/UPGMAAlgorithm.h:10: -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 51 | auto_ptr progSteps; - | ^~~~~~~~ -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -./tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 27 | auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, - | ^~~~~~~~ -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/../ClusterTree.h:20, @@ -654,8 +675,26 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp +./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, + | ^~~~~~~~ +In file included from /usr/include/c++/12/memory:76, + from ./tree/UPGMA/UPGMAAlgorithm.h:10: +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 51 | auto_ptr progSteps; + | ^~~~~~~~ +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +./tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 27 | auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, + | ^~~~~~~~ +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, @@ -666,17 +705,7 @@ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp -In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./tree/../alignment/Alignment.h:42, - from ./tree/Tree.h:13, - from ./tree/Tree.cpp:10: -./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, @@ -688,6 +717,18 @@ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp +In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./tree/../alignment/Alignment.h:42, + from ./tree/Tree.h:13, + from ./tree/Tree.cpp:10: +./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp ./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); @@ -712,6 +753,8 @@ | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, @@ -737,8 +780,36 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp +In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./tree/../alignment/Alignment.h:42, + from ./tree/ClusterTree.h:20, + from ./tree/UnRootedClusterTree.h:8, + from ./tree/UnRootedClusterTree.cpp:9: +./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +In file included from ./tree/ClusterTree.h:23: +./tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 26 | std::auto_ptr file; + | ^~~~~~~~ +In file included from /usr/include/c++/12/memory:76, + from ./tree/ClusterTree.h:16: +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +./tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 70 | auto_ptr quickDistMat; + | ^~~~~~~~ +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +./tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)': +./tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 164 | register int i; + | ^ In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/TreeInterface.h:19, @@ -903,32 +974,7 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./tree/../alignment/Alignment.h:42, - from ./tree/ClusterTree.h:20, - from ./tree/UnRootedClusterTree.h:8, - from ./tree/UnRootedClusterTree.cpp:9: -./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -In file included from ./tree/ClusterTree.h:23: -./tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 26 | std::auto_ptr file; - | ^~~~~~~~ -In file included from /usr/include/c++/12/memory:76, - from ./tree/ClusterTree.h:16: -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -./tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 70 | auto_ptr quickDistMat; - | ^~~~~~~~ -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTreeOutput.h:11, @@ -939,13 +985,6 @@ ./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"); | ^~~~~~~~~~~~~~ -./tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)': -./tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 164 | register int i; - | ^ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, @@ -1021,13 +1060,13 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp ./interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': ./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()); | ~~~~~~^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, @@ -1103,7 +1142,7 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, @@ -1125,15 +1164,12 @@ ./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 ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./multipleAlign/../alignment/Alignment.h:42, - from ./multipleAlign/ProfileAlignAlgorithm.h:10, - from ./multipleAlign/MyersMillerProfileAlign.h:10, - from ./multipleAlign/MyersMillerProfileAlign.cpp:10: -./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp +In file included from ./substitutionMatrix/SubMatrix.cpp:15: +./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"); | ^~~~~~~~~~~~~~ -./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +./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 ./multipleAlign/Iteration.cpp:17: @@ -1181,13 +1217,23 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from ./substitutionMatrix/SubMatrix.cpp:15: -./substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp +./multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': +./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 231 | tmpnam (buffer); + | ~~~~~~~^~~~~~~~ +In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./multipleAlign/../alignment/Alignment.h:42, + from ./multipleAlign/ProfileAlignAlgorithm.h:10, + from ./multipleAlign/MyersMillerProfileAlign.h:10, + from ./multipleAlign/MyersMillerProfileAlign.cpp:10: +./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"); | ^~~~~~~~~~~~~~ -./substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileStandard.h:9, @@ -1198,10 +1244,6 @@ ./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"); | ^~~~~~~~~~~~~~ -./multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': -./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 231 | tmpnam (buffer); - | ~~~~~~~^~~~~~~~ In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileWithSub.h:9, @@ -1212,10 +1254,6 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, @@ -1226,6 +1264,9 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/LowScoreSegProfile.h:13, @@ -1236,6 +1277,7 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp In file included from ./general/OutputFile.cpp:9: ./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; @@ -1245,22 +1287,19 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp ./general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)': ./general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 475 | register int i; | ^ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp ./general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)': ./general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 53 | register int p; | ^ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp ./general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)': ./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); @@ -1269,7 +1308,10 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp ./general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const': ./general/ClustalWResources.cpp:105:14: warning: writing 2 bytes into a region of size 1 [-Wstringop-overflow=] 105 | delim[0] = DIRDELIM; @@ -1277,6 +1319,8 @@ ./general/ClustalWResources.cpp:104:10: note: destination object 'delim' of size 1 104 | char delim[1]; | ^~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp In file included from ./general/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./general/../alignment/Alignment.h:42, from ./general/Stats.cpp:15: @@ -1286,9 +1330,6 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, @@ -1516,15 +1557,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, - from ./alignment/Alignment.h:42, - from ./main.cpp:10: -./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"); - | ^~~~~~~~~~~~~~ -./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"); - | ^~~~~~~~~~~~~~ ./Clustal.cpp: In member function 'void clustalw::Clustal::align(std::string*, bool)': ./Clustal.cpp:162:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 162 | auto_ptr progSteps; @@ -1539,6 +1571,15 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, + from ./alignment/Alignment.h:42, + from ./main.cpp:10: +./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"); + | ^~~~~~~~~~~~~~ +./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 ./main.cpp:16: ./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); @@ -1687,8 +1728,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'clustalw-dbgsym' in '../clustalw-dbgsym_2.1+lgpl-7_arm64.deb'. dpkg-deb: building package 'clustalw' in '../clustalw_2.1+lgpl-7_arm64.deb'. +dpkg-deb: building package 'clustalw-dbgsym' in '../clustalw-dbgsym_2.1+lgpl-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../clustalw_2.1+lgpl-7_arm64.buildinfo dpkg-genchanges --build=binary -O../clustalw_2.1+lgpl-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1696,12 +1737,14 @@ 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/7856/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/7856/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/18533 and its subdirectories -I: Current time: Fri Apr 21 16:59:56 -12 2023 -I: pbuilder-time-stamp: 1682139596 +I: removing directory /srv/workspace/pbuilder/7856 and its subdirectories +I: Current time: Sat May 25 01:25:24 +14 2024 +I: pbuilder-time-stamp: 1716549924