Diff of the two buildlogs: -- --- b1/build.log 2021-06-25 12:56:57.599544615 +0000 +++ b2/build.log 2021-06-25 12:59:16.190291320 +0000 @@ -1,8 +1,6 @@ -unshare: unshare failed: Cannot allocate memory -W: pbuilder: unshare CLONE_NEWNET not available -I: pbuilder: network access is available during build! -I: Current time: Fri Jun 25 00:50:28 -12 2021 -I: pbuilder-time-stamp: 1624625428 +I: pbuilder: network access will be disabled during build +I: Current time: Fri Jul 29 09:20:00 +14 2022 +I: pbuilder-time-stamp: 1659036000 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -19,8 +17,8 @@ I: copying [./clustalx_2.1+lgpl-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.19IdXkbZ/trustedkeys.kbx': General error -gpgv: Signature made Fri Dec 4 10:20:42 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.qWajUZyr/trustedkeys.kbx': General error +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 @@ -34,137 +32,171 @@ dpkg-source: info: applying qt5.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6629/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/50900/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/50900/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/50900/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='32b6dd0b7dbe4f16baa0c620d7db4f07' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='6629' - PS1='# ' - PS2='> ' + INVOCATION_ID=29a404c5af1147b2b47c6443e941b0db + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-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=50900 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/tmp.BZhxVoBwgA/pbuilderrc_GEY9 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.BZhxVoBwgA/b1 --logfile b1/build.log clustalx_2.1+lgpl-9.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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/tmp.BZhxVoBwgA/pbuilderrc_23av --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.BZhxVoBwgA/b2 --logfile b2/build.log --extrapackages usrmerge clustalx_2.1+lgpl-9.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-1 (2021-06-10) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux I: ls -l /bin total 5776 - -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 23 21:28 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/6629/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1367848 Jun 22 2021 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 29 09:20 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 29 05:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/50900/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -389,7 +421,7 @@ Get: 181 http://deb.debian.org/debian bullseye/main i386 qtbase5-dev-tools i386 5.15.2+dfsg-7 [846 kB] Get: 182 http://deb.debian.org/debian bullseye/main i386 qtbase5-dev i386 5.15.2+dfsg-7 [1152 kB] Get: 183 http://deb.debian.org/debian bullseye/main i386 qttools5-dev-tools i386 5.15.2-5 [1086 kB] -Fetched 124 MB in 20s (6068 kB/s) +Fetched 124 MB in 3s (37.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) @@ -1142,8 +1174,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (1901 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 28554 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. 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 +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 dpkg-buildpackage: info: source package clustalx dpkg-buildpackage: info: source version 2.1+lgpl-9 dpkg-buildpackage: info: source distribution unstable @@ -1173,7 +1241,7 @@ -e "s:LFLAGS *= .*:& -Wl,-z,relro -Wl,-z,now:" Makefile make[1]: Leaving directory '/build/clustalx-2.1+lgpl' dh_auto_build - make -j10 + make -j18 make[1]: Entering directory '/build/clustalx-2.1+lgpl' g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp @@ -1185,6 +1253,14 @@ g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] 74 | // tr("colorrules not found in the parameter file, using\ | ^ @@ -1238,8 +1314,6 @@ ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 251 | if(colorNum > 0 && colorNum - 1 < colorPar.size()) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1251,73 +1325,201 @@ 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] +In file included from main.cpp:21: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -In file included from AlignOutputFileNames.cpp:26: -AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 106 | auto_ptr outFileNames; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from AlignOutputFileNames.cpp:16: +In file included from clustalW/Clustal.h:18, + from mainwindow.h:45, + from main.cpp:24: +clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from ColumnScoreParams.cpp:23: -clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 75 | auto_ptr clustalOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 76 | auto_ptr gcgOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 77 | auto_ptr nbrfOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 78 | auto_ptr phylipOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 79 | auto_ptr gdeOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 80 | auto_ptr nexusOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/Clustal.h:20, + from mainwindow.h:45, + from main.cpp:24: +clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 81 | auto_ptr fastaOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/substitutionMatrix/../general/SquareMat.h:9, + from clustalW/substitutionMatrix/../general/clustalw.h:43, + from clustalW/substitutionMatrix/SubMatrix.h:28, + from main.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, - from BootstrapTreeDialog.h:11, - from BootstrapTreeDialog.cpp:18: + from HelpDisplayWidget.h:18, + from HelpDisplayWidget.cpp:15: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from PostscriptFileParams.h:4, + from PostscriptFileParams.cpp:1: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)': -ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] - 51 | void ColumnScoreParams::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ -In file included from BootstrapTreeDialog.cpp:18: -BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 70 | auto_ptr treeFileNames; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from BootstrapTreeDialog.cpp:8: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, @@ -1328,6 +1530,14 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +In file included from clustalW/substitutionMatrix/globalmatrix.h:8, + from PairwiseParams.cpp:23: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ In file included from AlignmentWidget.cpp:49: AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)': AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder] @@ -1339,6 +1549,10 @@ AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] 65 | AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) | ^~~~~~~~~~~~~~~ +PairwiseParams.cpp: In member function 'virtual void PairwiseParams::showEvent(QShowEvent*)': +PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] + 74 | void PairwiseParams::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ 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++) @@ -1463,193 +1677,19 @@ /usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ -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] +In file included from clustalW/substitutionMatrix/globalmatrix.h:8, + from LowScoringSegParams.cpp:22: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 75 | auto_ptr clustalOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 76 | auto_ptr gcgOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 77 | auto_ptr nbrfOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 78 | auto_ptr phylipOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 79 | auto_ptr gdeOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 80 | auto_ptr nexusOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from AlignmentViewerWidget.cpp:68: -clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 81 | auto_ptr fastaOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, - from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, - from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignmentViewerWidget.cpp:63: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': -AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 588 | for(i = 0; i < len && i < gapMask->size(); i++) - | ~~^~~~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': -AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 645 | for (i = 0; i < len && i < _secStructMask->size();i++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 652 | for(i = 0; i < len && i < ssMask.size(); i++) - | ~~^~~~~~~~~~~~~~~ -AlignmentViewerWidget.cpp: In member function 'virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)': -AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] - 781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) - | ~~~~~~~~~~~~~~~^~~~~ +LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': +LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] + 51 | void LowScoringSegParams::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1663,234 +1703,33 @@ 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/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 ClustalQtParams.h:13, - from HelpDisplayWidget.h:18, - from HelpDisplayWidget.cpp:15: + from AlignOutputFileNames.h:10, + from AlignOutputFileNames.cpp:26: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp -In file included from main.cpp:21: -clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-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; - | ^~~~~~ -In file included from clustalW/Clustal.h:18, - from mainwindow.h:45, - from main.cpp:24: -clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 75 | auto_ptr clustalOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 76 | auto_ptr gcgOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 77 | auto_ptr nbrfOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 78 | auto_ptr phylipOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 79 | auto_ptr gdeOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 80 | auto_ptr nexusOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/Clustal.h:20, - from mainwindow.h:45, - from main.cpp:24: -clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 81 | auto_ptr fastaOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/substitutionMatrix/../general/SquareMat.h:9, - from clustalW/substitutionMatrix/../general/clustalw.h:43, - from clustalW/substitutionMatrix/SubMatrix.h:28, - from main.cpp:21: +In file included from AlignOutputFileNames.cpp:26: +AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 106 | auto_ptr outFileNames; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from AlignOutputFileNames.cpp:16: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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 PostscriptFileParams.h:4, - from PostscriptFileParams.cpp:1: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 180 | if(column >= 0 && column < arrayOfHeights->size()) @@ -1922,35 +1761,77 @@ /usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp +ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] + 85 | QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ +ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] + 138 | void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ +ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)': +ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] + 175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from LowScoringSegParams.cpp:22: + from ColumnScoreParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': -LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] - 51 | void LowScoringSegParams::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ +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; + | ^~~~~~ +ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)': +ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] + 51 | void ColumnScoreParams::showEvent(QShowEvent* event) + | ~~~~~~~~~~~~^~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from BootstrapTreeDialog.h:11, + from BootstrapTreeDialog.cpp:18: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +In file included from BootstrapTreeDialog.cpp:18: +BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 70 | auto_ptr treeFileNames; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from BootstrapTreeDialog.cpp:8: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from PairwiseParams.cpp:23: + from AlignmentParameters.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -PairwiseParams.cpp: In member function 'virtual void PairwiseParams::showEvent(QShowEvent*)': -PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] - 74 | void PairwiseParams::showEvent(QShowEvent* event) - | ~~~~~~~~~~~~^~~~~ +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, @@ -1962,6 +1843,16 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from AlignmentViewerWidget.h:36, + from 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/Clustal.h:18, from mainwindow.h:45, from mainwindow.cpp:98: @@ -2242,58 +2133,205 @@ mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] 1454 | void MainWindow::writeViewer1AsPostscript(int type) | ~~~~^~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 75 | auto_ptr clustalOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 76 | auto_ptr gcgOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 77 | auto_ptr nbrfOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 78 | auto_ptr phylipOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 79 | auto_ptr gdeOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 80 | auto_ptr nexusOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from AlignmentViewerWidget.cpp:68: +clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 81 | auto_ptr fastaOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtCore/qdebug.h:54, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborcommon.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborvalue.h:45, + from /usr/include/i386-linux-gnu/qt5/QtCore/qcborarray.h:43, + from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:38, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignmentViewerWidget.cpp:63: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': +AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 588 | for(i = 0; i < len && i < gapMask->size(); i++) + | ~~^~~~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': +AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 645 | for (i = 0; i < len && i < _secStructMask->size();i++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 652 | for(i = 0; i < len && i < ssMask.size(); i++) + | ~~^~~~~~~~~~~~~~~ +AlignmentViewerWidget.cpp: In member function 'virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)': +AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] + 781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) + | ~~~~~~~~~~~~~~~^~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from PSPrinter.h:11, - from PSPrinter.cpp:20: + from clustalW/alignment/Alignment.cpp:25: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': -PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 207 | if(res.isLetter() && resNumber.size() > i - data->firstSeq) - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 307 | if(res.isLetter() && resNumber.size() > seq) - | ~~~~~~~~~~~~~~~~~^~~~~ -PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 421 | if(res.isLetter() && resNumber.size() > i) - | ~~~~~~~~~~~~~~~~~^~~ -PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] - 55 | int err; - | ^~~ -PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] - 73 | int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local - | ^~~~~~~ -PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] - 74 | int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local - | ^~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp -PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)': -PSPrinter.cpp:587:32: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 587 | if(data->nameHeader.size() > ix) - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp -PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': -PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] - 730 | for(i = fr; i <= lr && i < ruler.length(); i++) - | ~~^~~~~~~~~~~~~~~~ -PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)': -PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 789 | for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] - 781 | int psX, psY, curveBottom; - | ^~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp +clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)': +clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable] + 1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin(); + | ^~~~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.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, @@ -2581,189 +2619,27 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-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, - from SaveSeqFile.h:9, - from SaveSeqFile.cpp:23: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 75 | auto_ptr clustalOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 76 | auto_ptr gcgOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 77 | auto_ptr nbrfOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 78 | auto_ptr phylipOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 79 | auto_ptr gdeOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 80 | auto_ptr nexusOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from SaveSeqFile.cpp:26: -clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 81 | auto_ptr fastaOutFile; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from SaveSeqFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from SeqNameWidget.h:41, - from SeqNameWidget.cpp:59: + from HardCodedColorScheme.h:8, + from ColorParameters.h:11, + from PSPrinter.h:11, + from PSPrinter.cpp:20: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)': -SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable] - 375 | QRect redrawRect = event->rect(); - | ^~~~~~~~~~ -SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()': -SeqNameWidget.cpp:443:65: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] - 443 | int length = fontMetrics.width(QString(name.c_str())); - | ^ -In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QtGui:26, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from SeqNameWidget.cpp:58: -/usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here - 106 | int width(const QString &, int len = -1) const; - | ^~~~~ +PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': +PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 207 | if(res.isLetter() && resNumber.size() > i - data->firstSeq) + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 307 | if(res.isLetter() && resNumber.size() > seq) + | ~~~~~~~~~~~~~~~~~^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from clustalW/alignment/AlignmentOutput.h:24, @@ -2774,6 +2650,18 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 421 | if(res.isLetter() && resNumber.size() > i) + | ~~~~~~~~~~~~~~~~~^~~ +PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] + 55 | int err; + | ^~~ +PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] + 73 | int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local + | ^~~~~~~ +PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] + 74 | int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local + | ^~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); @@ -2913,80 +2801,49 @@ clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 2102 | catch(exception e) | ^ +PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)': +PSPrinter.cpp:587:32: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 587 | if(data->nameHeader.size() > ix) + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 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) | ^ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from clustalW/alignment/Alignment.cpp:25: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)': -clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable] - 1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin(); - | ^~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from TreeOutputFileNames.h:10, - from TreeOutputFileNames.cpp:17: + 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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp -In file included from TreeOutputFileNames.cpp:17: -TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 73 | auto_ptr treeFileNames; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from TreeOutputFileNames.cpp:7: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ +PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': +PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] + 730 | for(i = fr; i <= lr && i < ruler.length(); i++) + | ~~^~~~~~~~~~~~~~~~ +PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)': +PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 789 | for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] + 781 | int psX, psY, curveBottom; + | ^~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, - from WritePostscriptFile.h:10, - from WritePostscriptFile.cpp:24: + from SaveSeqFile.h:9, + from SaveSeqFile.cpp:23: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -In file included from WritePostscriptFile.cpp:24: -WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 88 | auto_ptr params; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, - from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, - from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, - from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ @@ -2998,11 +2855,11 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ @@ -3014,11 +2871,11 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ @@ -3030,11 +2887,11 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ @@ -3046,11 +2903,11 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ @@ -3062,11 +2919,11 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ @@ -3078,11 +2935,11 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ @@ -3094,11 +2951,11 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ @@ -3110,11 +2967,11 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from WritePostscriptFile.cpp:27: +In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ @@ -3126,22 +2983,10 @@ from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, - from WritePostscriptFile.cpp:14: + from SaveSeqFile.cpp:14: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp @@ -3156,6 +3001,7 @@ clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp In file included from clustalW/fileInput/FileReader.cpp:29: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); @@ -3166,7 +3012,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp clustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)': clustalW/fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 155 | auto_ptr fileParser; // Means we dont need to delete it! @@ -3193,6 +3038,8 @@ | ^~ g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual std::vector clustalw::MSFFileParser::getSeqRange(int, int, std::string*)': clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter] 34 | vector MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) @@ -3210,6 +3057,33 @@ clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter] 247 | string& secStructName, int &structPenalties, int length) | ~~~~^~~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from TreeOutputFileNames.h:10, + from TreeOutputFileNames.cpp:17: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +In file included from TreeOutputFileNames.cpp:17: +TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 73 | auto_ptr treeFileNames; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from TreeOutputFileNames.cpp:7: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ 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) @@ -3227,7 +3101,14 @@ clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] 446 | int &structPenalties, int length) | ~~~~^~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.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, @@ -3241,15 +3122,7 @@ clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter] 293 | string& secStructName, int &structPenalties, int length) | ~~~~^~~~~~ -clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': -clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] - 240 | void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.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; @@ -3257,9 +3130,7 @@ clustalW/general/ClustalWResources.cpp:104:10: note: while referencing 'delim' 104 | char delim[1]; | ^~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp In file included from clustalW/general/OutputFile.cpp:9: clustalW/general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; @@ -3270,9 +3141,211 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from SeqNameWidget.h:41, + from SeqNameWidget.cpp:59: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~ +SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)': +SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable] + 375 | QRect redrawRect = event->rect(); + | ^~~~~~~~~~ +SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()': +SeqNameWidget.cpp:443:65: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] + 443 | int length = fontMetrics.width(QString(name.c_str())); + | ^ +In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QtGui:26, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from SeqNameWidget.cpp:58: +/usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here + 106 | int width(const QString &, int len = -1) const; + | ^~~~~ +In file included from WritePostscriptFile.cpp:24: +WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 88 | auto_ptr params; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 75 | auto_ptr clustalOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 76 | auto_ptr gcgOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 77 | auto_ptr nbrfOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 78 | auto_ptr phylipOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 79 | auto_ptr gdeOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 80 | auto_ptr nexusOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from WritePostscriptFile.cpp:27: +clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 81 | auto_ptr fastaOutFile; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, + from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48, + from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, + from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1, + from WritePostscriptFile.cpp:14: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp +clustalW/general/UserParameters.cpp: In constructor 'clustalw::UserParameters::UserParameters(bool)': +clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter] + 33 | UserParameters::UserParameters(bool log) + | ~~~~~^~~ In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/general/../alignment/Alignment.h:42, from clustalW/general/Stats.cpp:15: @@ -3282,10 +3355,7 @@ 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"); | ^~~~~~~~~~~~~~ -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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)': clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable] 251 | int n; @@ -3294,6 +3364,8 @@ clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] 519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) | ~~~~~~~~^~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.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); @@ -3302,20 +3374,111 @@ 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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-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/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] +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/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +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/Iteration.cpp:17: +clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/multipleAlign/Iteration.cpp:17: +clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/multipleAlign/Iteration.cpp:17: +clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/multipleAlign/Iteration.cpp:17: +clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/multipleAlign/Iteration.cpp:17: +clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/multipleAlign/Iteration.cpp:17: +clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/multipleAlign/Iteration.cpp:17: +clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': +clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] + 170 | int count; + | ^~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/LowScoreSegProfile.h:13, @@ -3326,6 +3489,22 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 231 | tmpnam (buffer); + | ~~~~~~~^~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.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/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"); + | ^~~~~~~~~~~~~~ In file included from clustalW/interface/../Clustal.h:18, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: @@ -3498,109 +3677,15 @@ | ^~~~~~~~ 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: + from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, + from clustalW/multipleAlign/MyersMillerProfileAlign.h:10, + from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -In file included from clustalW/multipleAlign/Iteration.cpp:17: -clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/multipleAlign/Iteration.cpp:17: -clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/multipleAlign/Iteration.cpp:17: -clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/multipleAlign/Iteration.cpp:17: -clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/multipleAlign/Iteration.cpp:17: -clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/multipleAlign/Iteration.cpp:17: -clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/multipleAlign/Iteration.cpp:17: -clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': -clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] - 170 | int count; - | ^~~~~ 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, @@ -3613,6 +3698,7 @@ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp In file included from clustalW/interface/../Clustal.h:18, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: @@ -3743,36 +3829,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()': -clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] - 41 | catch(bad_alloc) - | ^~~~~~~~~ -clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 231 | tmpnam (buffer); - | ~~~~~~~^~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp -clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()': -clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] - 520 | clustalObj->getHelp('C'); - | ~~~~~~~~~~~~~~~~~~~^~~~~ -clustalW/interface/InteractiveMenu.cpp:521:13: note: here - 521 | case 'Q': - | ^~~~ -clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': -clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1190 | system(lin1.c_str()); - | ~~~~~~^~~~~~~~~~~~~~ -In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, - from clustalW/multipleAlign/MyersMillerProfileAlign.h:10, - from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: -clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, @@ -3784,6 +3840,10 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()': +clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] + 41 | catch(bad_alloc) + | ^~~~~~~~~ clustalW/multipleAlign/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 @@ -3792,39 +3852,48 @@ clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] 359 | string phylipName) | ~~~~~~~^~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/ProfileBase.h:14, - from clustalW/multipleAlign/ProfileBase.cpp:9: + from clustalW/multipleAlign/ProfileStandard.h:9, + from clustalW/multipleAlign/ProfileStandard.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp +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()); + | ~~~~~~^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/ProfileStandard.h:9, - from clustalW/multipleAlign/ProfileStandard.cpp:9: + from clustalW/multipleAlign/ProfileBase.h:14, + from clustalW/multipleAlign/ProfileBase.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/pairwise/../alignment/Alignment.h:42, - from clustalW/pairwise/PairwiseAlignBase.h:10, - from clustalW/pairwise/FullPairwiseAlign.h:9, - from clustalW/pairwise/FullPairwiseAlign.cpp:9: -clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.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/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, @@ -3837,33 +3906,6 @@ 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"); | ^~~~~~~~~~~~~~ -In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/pairwise/../alignment/Alignment.h:42, - from clustalW/pairwise/PairwiseAlignBase.h:10, - from clustalW/pairwise/FastPairwiseAlign.h:9, - from clustalW/pairwise/FastPairwiseAlign.cpp:10: -clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.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"); - | ^~~~~~~~~~~~~~ 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) @@ -3879,18 +3921,17 @@ 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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp -In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/tree/../alignment/Alignment.h:42, - from clustalW/tree/ClusterTreeOutput.h:11, - from clustalW/tree/ClusterTreeOutput.cpp:9: -clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/pairwise/../alignment/Alignment.h:42, + from clustalW/pairwise/PairwiseAlignBase.h:10, + from clustalW/pairwise/FastPairwiseAlign.h:9, + from clustalW/pairwise/FastPairwiseAlign.cpp:10: +clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTree.h:20, @@ -3901,6 +3942,7 @@ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp In file included from clustalW/tree/ClusterTree.h:23, from clustalW/tree/ClusterTree.cpp:9: clustalW/tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -3922,97 +3964,39 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/tree/../alignment/Alignment.h:42, - from clustalW/tree/Tree.h:13, - from clustalW/tree/Tree.cpp:10: -clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)': +clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable] + 580 | int rs = 0, rl = 0; + | ^~ +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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp +In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/pairwise/../alignment/Alignment.h:42, + from clustalW/pairwise/PairwiseAlignBase.h:10, + from clustalW/pairwise/FullPairwiseAlign.h:9, + from clustalW/pairwise/FullPairwiseAlign.cpp:9: +clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, - from clustalW/tree/ClusterTree.h:20, - from clustalW/tree/UnRootedClusterTree.h:8, - from clustalW/tree/UnRootedClusterTree.cpp:9: + from clustalW/tree/ClusterTreeOutput.h:11, + from clustalW/tree/ClusterTreeOutput.cpp:9: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)': -clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable] - 580 | int rs = 0, rl = 0; - | ^~ -clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] - 580 | int rs = 0, rl = 0; - | ^~ -In file included from clustalW/tree/ClusterTree.h:23, - from clustalW/tree/UnRootedClusterTree.h:8, - from clustalW/tree/UnRootedClusterTree.cpp:9: -clustalW/tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 26 | std::auto_ptr file; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from clustalW/tree/ClusterTree.h:16, - from clustalW/tree/UnRootedClusterTree.h:8, - from clustalW/tree/UnRootedClusterTree.cpp:9: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/tree/UnRootedClusterTree.h:8, - from clustalW/tree/UnRootedClusterTree.cpp:9: -clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 70 | auto_ptr quickDistMat; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from clustalW/tree/ClusterTree.h:16, - from clustalW/tree/UnRootedClusterTree.h:8, - from clustalW/tree/UnRootedClusterTree.cpp:9: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from clustalW/tree/Tree.cpp:10: -clustalW/tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 26 | auto_ptr createSets(int firstSeq, int lastSeq); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/tree/../alignment/Alignment.h:38, - from clustalW/tree/Tree.h:13, - from clustalW/tree/Tree.cpp:10: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -clustalW/tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 278 | auto_ptr Tree::createSets(int firstSeq, int lastSeq) - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/tree/../alignment/Alignment.h:38, - from clustalW/tree/Tree.h:13, - from clustalW/tree/Tree.cpp:10: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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 [-Wdeprecated-declarations] - 280 | auto_ptr progAlignSteps; - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from clustalW/tree/../alignment/Alignment.h:38, - from clustalW/tree/Tree.h:13, - from clustalW/tree/Tree.cpp:10: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/TreeInterface.h:19, @@ -4093,6 +4077,16 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/tree/../alignment/Alignment.h:42, + from clustalW/tree/Tree.h:13, + from clustalW/tree/Tree.cpp:10: +clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/TreeInterface.cpp:17: @@ -4126,6 +4120,7 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp In file included from clustalW/tree/TreeInterface.cpp:23: clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, @@ -4253,8 +4248,50 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp +In file included from clustalW/tree/Tree.cpp:10: +clustalW/tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 26 | auto_ptr createSets(int firstSeq, int lastSeq); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/tree/../alignment/Alignment.h:38, + from clustalW/tree/Tree.h:13, + from clustalW/tree/Tree.cpp:10: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +clustalW/tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 278 | auto_ptr Tree::createSets(int firstSeq, int lastSeq) + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/tree/../alignment/Alignment.h:38, + from clustalW/tree/Tree.h:13, + from clustalW/tree/Tree.cpp:10: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | 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 [-Wdeprecated-declarations] + 280 | auto_ptr progAlignSteps; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from clustalW/tree/../alignment/Alignment.h:38, + from clustalW/tree/Tree.h:13, + from clustalW/tree/Tree.cpp:10: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp +g++ -pipe -g -O2 -fdebug-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/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/../ClusterTree.h:20, @@ -4345,9 +4382,44 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp -g++ -pipe -g -O2 -fdebug-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/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp +In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/tree/../alignment/Alignment.h:42, + from clustalW/tree/ClusterTree.h:20, + from clustalW/tree/UnRootedClusterTree.h:8, + from clustalW/tree/UnRootedClusterTree.cpp:9: +clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +In file included from clustalW/tree/ClusterTree.h:23, + from clustalW/tree/UnRootedClusterTree.h:8, + from clustalW/tree/UnRootedClusterTree.cpp:9: +clustalW/tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 26 | std::auto_ptr file; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from clustalW/tree/ClusterTree.h:16, + from clustalW/tree/UnRootedClusterTree.h:8, + from clustalW/tree/UnRootedClusterTree.cpp:9: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from clustalW/tree/UnRootedClusterTree.h:8, + from clustalW/tree/UnRootedClusterTree.cpp:9: +clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 70 | auto_ptr quickDistMat; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from clustalW/tree/ClusterTree.h:16, + from clustalW/tree/UnRootedClusterTree.h:8, + from clustalW/tree/UnRootedClusterTree.cpp:9: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | 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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.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, @@ -4359,10 +4431,7 @@ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)': -clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: 'n' may be used uninitialized in this function [-Wmaybe-uninitialized] - 1103 | return (maxRes); - | ^ +/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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.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, @@ -4373,6 +4442,15 @@ 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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include ProteinGapParameters.h -o moc_ProteinGapParameters.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, @@ -4384,7 +4462,9 @@ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -/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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include PSPrinter.h -o moc_PSPrinter.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.cpp +/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include SearchForString.h -o moc_SearchForString.cpp In file included from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, @@ -4426,22 +4506,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-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/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include ProteinGapParameters.h -o moc_ProteinGapParameters.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include PSPrinter.h -o moc_PSPrinter.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.cpp -/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include SearchForString.h -o moc_SearchForString.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include SecStructOptions.h -o moc_SecStructOptions.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include SeqNameWidget.h -o moc_SeqNameWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/10 -I/usr/include/i386-linux-gnu/c++/10 -I/usr/include/c++/10/backward -I/usr/lib/gcc/i686-linux-gnu/10/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include TreeFormatOptions.h -o moc_TreeFormatOptions.cpp @@ -4456,7 +4520,18 @@ g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.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 in this function [-Wmaybe-uninitialized] + 1103 | return (maxRes); + | ^ g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, @@ -4467,28 +4542,32 @@ 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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-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 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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.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 HelpDisplayWidget.h:18, + from moc_HelpDisplayWidget.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -In file included from moc_AlignOutputFileNames.cpp:10: -AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 106 | auto_ptr outFileNames; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from moc_AlignOutputFileNames.cpp:9: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -4500,7 +4579,6 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp In file included from moc_BootstrapTreeDialog.cpp:10: BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 70 | auto_ptr treeFileNames; @@ -4513,14 +4591,24 @@ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, - from HelpDisplayWidget.h:18, - from moc_HelpDisplayWidget.cpp:10: + from AlignOutputFileNames.h:10, + from moc_AlignOutputFileNames.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp +In file included from moc_AlignOutputFileNames.cpp:10: +AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 106 | auto_ptr outFileNames; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from moc_AlignOutputFileNames.cpp:9: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -4536,25 +4624,6 @@ | ^~~~~~~~~~~~~~ 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: -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 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:10: @@ -4564,31 +4633,6 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -fdebug-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 -fdebug-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/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from SaveSeqFile.h:9, - from moc_SaveSeqFile.cpp:10: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from PSPrinter.h:11, - from moc_PSPrinter.cpp:10: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ -clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); - | ^~~~~~~~~~~~~~ In file included from clustalW/Clustal.h:18, from mainwindow.h:45, from moc_mainwindow.cpp:10: @@ -4701,6 +4745,30 @@ | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from HardCodedColorScheme.h:8, + from ColorParameters.h:11, + from PSPrinter.h:11, + from moc_PSPrinter.cpp:10: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from SaveSeqFile.h:9, + from moc_SaveSeqFile.cpp:10: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); + | ^~~~~~~~~~~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from moc_SeqNameWidget.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -4786,12 +4854,15 @@ dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) +I: copying local configuration +I: user script /srv/workspace/pbuilder/50900/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/50900/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/6629 and its subdirectories -I: Current time: Fri Jun 25 00:56:57 -12 2021 -I: pbuilder-time-stamp: 1624625817 +I: removing directory /srv/workspace/pbuilder/50900 and its subdirectories +I: Current time: Fri Jul 29 09:22:15 +14 2022 +I: pbuilder-time-stamp: 1659036135