Diff of the two buildlogs: -- --- b1/build.log 2021-07-03 16:42:28.045582086 +0000 +++ b2/build.log 2021-07-03 16:44:00.774118876 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Aug 5 11:03:54 -12 2022 -I: pbuilder-time-stamp: 1659740634 +I: Current time: Sun Jul 4 06:42:29 +14 2021 +I: pbuilder-time-stamp: 1625330549 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Sun Feb 24 07:18:02 2019 -12 +gpgv: Signature made Mon Feb 25 09:18:02 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,136 +31,170 @@ dpkg-source: info: applying qt5.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/53490/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/61328/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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/61328/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/61328/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2cbeb0deab4b435687b6c98478a526b8' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='53490' - PS1='# ' - PS2='> ' + INVOCATION_ID=8730d1773d644e62ba988d0d48229b45 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=61328 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.Zu7HECKowB/pbuilderrc_O1Wh --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Zu7HECKowB/b1 --logfile b1/build.log clustalx_2.1+lgpl-8.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.Zu7HECKowB/pbuilderrc_kB2E --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Zu7HECKowB/b2 --logfile b2/build.log clustalx_2.1+lgpl-8.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 24 02:47 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/53490/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 4 06:42 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 21 22:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/61328/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -406,7 +440,7 @@ Get: 202 http://deb.debian.org/debian buster/main amd64 qtbase5-dev-tools amd64 5.11.3+dfsg1-1+deb10u4 [770 kB] Get: 203 http://deb.debian.org/debian buster/main amd64 qtbase5-dev amd64 5.11.3+dfsg1-1+deb10u4 [1014 kB] Get: 204 http://deb.debian.org/debian buster/main amd64 qttools5-dev-tools amd64 5.11.3-4 [1069 kB] -Fetched 103 MB in 2s (62.5 MB/s) +Fetched 103 MB in 1s (77.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -1251,7 +1285,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/clustalx-2.1+lgpl/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +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-8 dpkg-buildpackage: info: source distribution unstable @@ -1281,7 +1315,7 @@ -e "s:LFLAGS *= .*:& -Wl,-z,relro -Wl,-z,now:" Makefile make[1]: Leaving directory '/build/clustalx-2.1+lgpl' dh_auto_build - make -j16 + make -j15 make[1]: Entering directory '/build/clustalx-2.1+lgpl' g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp @@ -1298,7 +1332,6 @@ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] // tr("colorrules not found in the parameter file, using\ ^ @@ -1313,13 +1346,19 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -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] +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from HelpDisplayWidget.h:18, + from HelpDisplayWidget.cpp:15: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1370,8 +1409,22 @@ ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(colorNum > 0 && colorNum - 1 < colorPar.size()) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.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] + 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] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp +HelpDisplayWidget.cpp: In member function 'std::__cxx11::string* HelpDisplayWidget::loadHelpInformation(char)': +HelpDisplayWidget.cpp:147:29: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] + catch(ifstream::failure e) + ^ +HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] + int i, number, nlines; + ^~~~~~ In file included from clustalW/Clustal.h:18, from mainwindow.h:45, from main.cpp:24: @@ -1534,116 +1587,6 @@ ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from HelpDisplayWidget.h:18, - from HelpDisplayWidget.cpp:15: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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 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] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from AlignmentWidget.h:41, - from AlignmentWidget.cpp:49: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - 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] - bool blackAndWhite; - ^~~~~~~~~~~~~ -AlignmentWidget.h:161:27: warning: 'std::vector >* AlignmentWidget::selectedColoredRes' [-Wreorder] - std::vector* selectedColoredRes; - ^~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] - AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) - ^~~~~~~~~~~~~~~ -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] - for(unsigned int j = 0; j < lengthLongestSeq; j++) - ~~^~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:235:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(code >= 0 && code < conservationPixmaps->size()) - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:268:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) - ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:280:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size()) - ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:291:86: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j) - ~~~~~~~~~~~~~~~~~~~~~^~~ -AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable] - int codeForSpace = clustalw::userParameters->resIndex( - ^~~~~~~~~~~~ -AlignmentWidget.cpp: In member function 'void AlignmentWidget::generateSecStructurePixmaps()': -AlignmentWidget.cpp:333:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(i < secStructPixmaps->size() && i < secStructInfo.size()) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp: In member function 'void AlignmentWidget::drawContents(QPainter*, int, int, int, int)': -AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(selectedRes >= selectedColoredRes->size()) - ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()': -AlignmentWidget.cpp:689:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(int j = 1; j <= strongGroup.size(); j++) - ~~^~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:693:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(int j = 1; j <= weakGroup.size(); j++) - ~~^~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:700:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if((i + _fRes - 1 < (*alignment)[j].size()) && - ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:701:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - (i + _fRes - 1 < (*alignment)[_fSeq].size())) - ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:725:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(int k = 1; k <= strongGroup.size(); k++) - ~~^~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:737:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(int k = 1; k <= weakGroup.size(); k++) - ~~^~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:760:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(int k = 1; k <= strongGroup.size(); k++) - ~~^~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp:771:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(int k = 1; k <= weakGroup.size(); k++) - ~~^~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp: In member function 'void AlignmentWidget::makeColorMask(clustalw::Array2D*, ColorParameters*)': -AlignmentWidget.cpp:878:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) - ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()': -AlignmentWidget.cpp:927:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) - ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()': -AlignmentWidget.cpp:1039:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(int j = 0; j < aminoAcid.size(); j++) - ~~^~~~~~~~~~~~~~~~~~ -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] @@ -1652,18 +1595,13 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from BootstrapTreeDialog.h:11, - from BootstrapTreeDialog.cpp:18: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - 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 'long unsigned int'} [-Wsign-compare] + if(column >= 0 && column < arrayOfHeights->size()) + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if(column >= 0 && column < arrayOfHeights->size()) + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); @@ -1799,21 +1737,6 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -In file included from BootstrapTreeDialog.cpp:18: -BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr treeFileNames; - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from /usr/include/c++/8/thread:39, - from /usr/include/c++/8/future:39, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qthread.h:50, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:223, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from BootstrapTreeDialog.cpp:15: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(i = 0; i < len && i < gapMask->size(); i++) @@ -1832,29 +1755,96 @@ 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: + 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] 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] 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] - auto_ptr outFileNames; - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from /usr/include/c++/8/thread:39, - from /usr/include/c++/8/future:39, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qthread.h:50, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:223, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, - from AlignOutputFileNames.cpp:23: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from AlignmentWidget.h:41, + from AlignmentWidget.cpp:49: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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] + 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] + bool blackAndWhite; + ^~~~~~~~~~~~~ +AlignmentWidget.h:161:27: warning: 'std::vector >* AlignmentWidget::selectedColoredRes' [-Wreorder] + std::vector* selectedColoredRes; + ^~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] + AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) + ^~~~~~~~~~~~~~~ +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] + for(unsigned int j = 0; j < lengthLongestSeq; j++) + ~~^~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:235:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if(code >= 0 && code < conservationPixmaps->size()) + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:268:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) + ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:280:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size()) + ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:291:86: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j) + ~~~~~~~~~~~~~~~~~~~~~^~~ +AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable] + int codeForSpace = clustalw::userParameters->resIndex( + ^~~~~~~~~~~~ +AlignmentWidget.cpp: In member function 'void AlignmentWidget::generateSecStructurePixmaps()': +AlignmentWidget.cpp:333:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if(i < secStructPixmaps->size() && i < secStructInfo.size()) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp: In member function 'void AlignmentWidget::drawContents(QPainter*, int, int, int, int)': +AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if(selectedRes >= selectedColoredRes->size()) + ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()': +AlignmentWidget.cpp:689:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(int j = 1; j <= strongGroup.size(); j++) + ~~^~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:693:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(int j = 1; j <= weakGroup.size(); j++) + ~~^~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:700:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if((i + _fRes - 1 < (*alignment)[j].size()) && + ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:701:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + (i + _fRes - 1 < (*alignment)[_fSeq].size())) + ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:725:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(int k = 1; k <= strongGroup.size(); k++) + ~~^~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:737:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(int k = 1; k <= weakGroup.size(); k++) + ~~^~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:760:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(int k = 1; k <= strongGroup.size(); k++) + ~~^~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp:771:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(int k = 1; k <= weakGroup.size(); k++) + ~~^~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp: In member function 'void AlignmentWidget::makeColorMask(clustalw::Array2D*, ColorParameters*)': +AlignmentWidget.cpp:878:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) + ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()': +AlignmentWidget.cpp:927:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) + ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -1868,6 +1858,10 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()': +AlignmentWidget.cpp:1039:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(int j = 0; j < aminoAcid.size(); j++) + ~~^~~~~~~~~~~~~~~~~~ ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)': ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] QTreeWidgetItem *parentItem) @@ -1880,32 +1874,57 @@ ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) ~~~~~~~~~~~~~~~~~^~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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 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] + 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] + 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] + auto_ptr outFileNames; + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from /usr/include/c++/8/thread:39, + from /usr/include/c++/8/future:39, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qthread.h:50, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:223, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from AlignOutputFileNames.cpp:23: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ In file included from clustalW/substitutionMatrix/globalmatrix.h:8, - from ColumnScoreParams.cpp:23: + from LowScoringSegParams.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] 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] - void ColumnScoreParams::showEvent(QShowEvent* event) - ~~~~~~~~~~~~^~~~~ -HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)': -HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(column >= 0 && column < arrayOfHeights->size()) - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - if(column >= 0 && column < arrayOfHeights->size()) - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -HelpDisplayWidget.cpp: In member function 'std::__cxx11::string* HelpDisplayWidget::loadHelpInformation(char)': -HelpDisplayWidget.cpp:147:29: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] - catch(ifstream::failure e) - ^ -HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] - int i, number, nlines; - ^~~~~~ +LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': +LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] + void LowScoringSegParams::showEvent(QShowEvent* event) + ~~~~~~~~~~~~^~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from BootstrapTreeDialog.h:11, + from BootstrapTreeDialog.cpp:18: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ 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] @@ -1918,22 +1937,36 @@ AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter] void AlignmentParameters::showEvent(QShowEvent* event) ~~~~~~~~~~~~^~~~~ +In file included from BootstrapTreeDialog.cpp:18: +BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr treeFileNames; + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from /usr/include/c++/8/thread:39, + from /usr/include/c++/8/future:39, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qthread.h:50, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:223, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, + from BootstrapTreeDialog.cpp:15: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp 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] 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] 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] - void LowScoringSegParams::showEvent(QShowEvent* event) - ~~~~~~~~~~~~^~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp +ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)': +ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] + void ColumnScoreParams::showEvent(QShowEvent* event) + ~~~~~~~~~~~~^~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, @@ -1945,9 +1978,7 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp In file included from clustalW/Clustal.h:18, from mainwindow.h:45, from mainwindow.cpp:98: @@ -2186,7 +2217,12 @@ mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] void MainWindow::writeViewer1AsPostscript(int type) ~~~~^~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp 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] @@ -2199,58 +2235,7 @@ PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] void PairwiseParams::showEvent(QShowEvent* event) ~~~~~~~~~~~~^~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.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: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': -PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - if(res.isLetter() && resNumber.size() > i - data->firstSeq) - ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - if(res.isLetter() && resNumber.size() > seq) - ~~~~~~~~~~~~~~~~~^~~~~ -PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - if(res.isLetter() && resNumber.size() > i) - ~~~~~~~~~~~~~~~~~^~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp -PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] - int err; - ^~~ -PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] - int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local - ^~~~~~~ -PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] - int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local - ^~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.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 'long unsigned int'} and 'int' [-Wsign-compare] - if(data->nameHeader.size() > ix) - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp -PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': -PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(i = fr; i <= lr && i < ruler.length(); i++) - ~~^~~~~~~~~~~~~~~~ -PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)': -PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] - int psX, psY, curveBottom; - ^~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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, @@ -2551,7 +2536,49 @@ clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable] SeqArray::iterator posToAddTo = sectionToRealign.begin(); ^~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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 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] + 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] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': +PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + if(res.isLetter() && resNumber.size() > i - data->firstSeq) + ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + if(res.isLetter() && resNumber.size() > seq) + ~~~~~~~~~~~~~~~~~^~~~~ +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] + 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] + 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 'long unsigned int'} and 'int' [-Wsign-compare] + if(res.isLetter() && resNumber.size() > i) + ~~~~~~~~~~~~~~~~~^~~ +PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] + int err; + ^~~ +PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] + int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local + ^~~~~~~ +PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] + int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local + ^~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from clustalW/alignment/AlignmentOutput.h:24, @@ -2562,7 +2589,6 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp 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] bool openExplicitFile(auto_ptr& outFile, string fileName); @@ -2706,19 +2732,25 @@ clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/ObjectiveScore.h:15, - from clustalW/alignment/ObjectiveScore.cpp:10: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ +PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)': +PSPrinter.cpp:587:32: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + if(data->nameHeader.size() > ix) + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp +PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': +PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(i = fr; i <= lr && i < ruler.length(); i++) + ~~^~~~~~~~~~~~~~~~ +PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)': +PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] + int psX, psY, curveBottom; + ^~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -2865,72 +2897,22 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp -In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/fileInput/../alignment/Alignment.h:42, - from clustalW/fileInput/FileReader.h:12, - from clustalW/fileInput/FileReader.cpp:29: -clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +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] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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] - void checkInfile(int* nseqs, auto_ptr& fileParser); - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from clustalW/fileInput/FileReader.h:11, - from clustalW/fileInput/FileReader.cpp:29: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -clustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::__cxx11::string*)': -clustalW/fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr fileParser; // Means we dont need to delete it! - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from clustalW/fileInput/FileReader.h:11, - from clustalW/fileInput/FileReader.cpp:29: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -clustalW/fileInput/FileReader.cpp: At global scope: -clustalW/fileInput/FileReader.cpp:426:42: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from clustalW/fileInput/FileReader.h:11, - from clustalW/fileInput/FileReader.cpp:29: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -clustalW/fileInput/FileReader.cpp: In member function 'void clustalw::FileReader::checkInfile(int*, std::auto_ptr&)': -clustalW/fileInput/FileReader.cpp:555:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] - catch(exception ex) - ^~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp -clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::__cxx11::string*)': -clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter] - Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) - ~~~~~~~~^~~~~~~~~~~~ -clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': -clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] - void PearsonFileParser::getSecStructure(vector& gapPenaltyMask, - ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter] - vector& secStructMask, string& secStructName, - ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter] - vector& secStructMask, string& secStructName, - ~~~~~~~~^~~~~~~~~~~~~ -clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] - int &structPenalties, int length) - ~~~~^~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp +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] + QRect redrawRect = event->rect(); + ^~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -2957,47 +2939,25 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.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 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] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual std::vector clustalw::MSFFileParser::getSeqRange(int, int, std::__cxx11::string*)': -clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter] - vector MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) - ~~~~~~~~^~~~~~~~~~~~ -clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual void clustalw::MSFFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': -clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] - void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, - ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] - void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, - ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter] - string& secStructName, int &structPenalties, int length) - ~~~~~~~~^~~~~~~~~~~~~ -clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter] - string& secStructName, int &structPenalties, int length) - ~~~~^~~~~~ -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] - QRect redrawRect = event->rect(); - ^~~~~~~~~~ -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] +In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/fileInput/../alignment/Alignment.h:42, + from clustalW/fileInput/FileReader.h:12, + from clustalW/fileInput/FileReader.cpp:29: +clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from WritePostscriptFile.cpp:24: @@ -3015,19 +2975,40 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -clustalW/fileInput/PIRFileParser.cpp: In member function 'virtual void clustalw::PIRFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': -clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] - void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, - ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -clustalW/fileInput/PIRFileParser.cpp:292:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] - void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, - ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -clustalW/fileInput/PIRFileParser.cpp:293:45: warning: unused parameter 'secStructName' [-Wunused-parameter] - string& secStructName, int &structPenalties, int length) - ~~~~~~~~^~~~~~~~~~~~~ -clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter] - string& secStructName, int &structPenalties, int length) - ~~~~^~~~~~ +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] + void checkInfile(int* nseqs, auto_ptr& fileParser); + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from clustalW/fileInput/FileReader.h:11, + from clustalW/fileInput/FileReader.cpp:29: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +clustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::__cxx11::string*)': +clustalW/fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr fileParser; // Means we dont need to delete it! + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from clustalW/fileInput/FileReader.h:11, + from clustalW/fileInput/FileReader.cpp:29: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +clustalW/fileInput/FileReader.cpp: At global scope: +clustalW/fileInput/FileReader.cpp:426:42: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from clustalW/fileInput/FileReader.h:11, + from clustalW/fileInput/FileReader.cpp:29: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +clustalW/fileInput/FileReader.cpp: In member function 'void clustalw::FileReader::checkInfile(int*, std::auto_ptr&)': +clustalW/fileInput/FileReader.cpp:555:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] + catch(exception ex) + ^~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); @@ -3163,21 +3144,67 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp -clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': -clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] - void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, +clustalW/fileInput/PIRFileParser.cpp: In member function 'virtual void clustalw::PIRFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': +clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] + void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +clustalW/fileInput/PIRFileParser.cpp:292:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] + void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, + ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/PIRFileParser.cpp:293:45: warning: unused parameter 'secStructName' [-Wunused-parameter] + string& secStructName, int &structPenalties, int length) + ~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter] + string& secStructName, int &structPenalties, int length) + ~~~~^~~~~~ clustalW/general/ClustalWResources.cpp: In member function 'std::__cxx11::string clustalw::ClustalWResources::findFile(std::__cxx11::string, clustalw::ClustalWResourcePathType) const': clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript 1 is above array bounds of 'char [1]' [-Warray-bounds] delim[1] = 0; ~~~~~~~^ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp +clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual std::vector clustalw::MSFFileParser::getSeqRange(int, int, std::__cxx11::string*)': +clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter] + vector MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) + ~~~~~~~~^~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::__cxx11::string*)': +clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter] + Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) + ~~~~~~~~^~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': +clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] + void PearsonFileParser::getSecStructure(vector& gapPenaltyMask, + ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter] + vector& secStructMask, string& secStructName, + ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter] + vector& secStructMask, string& secStructName, + ~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] + int &structPenalties, int length) + ~~~~^~~~~~ +clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual void clustalw::MSFFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': +clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] + void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, + ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] + void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, + ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter] + string& secStructName, int &structPenalties, int length) + ~~~~~~~~^~~~~~~~~~~~~ +clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter] + string& secStructName, int &structPenalties, int length) + ~~~~^~~~~~ 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] std::auto_ptr file; @@ -3188,7 +3215,12 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp +clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': +clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] + void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, + ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/general/../alignment/Alignment.h:42, from clustalW/general/Stats.cpp:15: @@ -3198,14 +3230,14 @@ clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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] - UserParameters::UserParameters(bool log) - ~~~~~^~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.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] int n; @@ -3214,7 +3246,6 @@ clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) ~~~~~~~~^~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.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] fgets(line, MAXLINE, stdin); @@ -3223,7 +3254,12 @@ clustalW/general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp +clustalW/general/UserParameters.cpp: In constructor 'clustalw::UserParameters::UserParameters(bool)': +clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter] + UserParameters::UserParameters(bool log) + ~~~~~^~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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, @@ -3406,7 +3442,6 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/LowScoreSegProfile.h:13, @@ -3417,108 +3452,6 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp -In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/multipleAlign/../alignment/Alignment.h:42, - from clustalW/multipleAlign/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] - 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] - 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] - auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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] - auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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] - auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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] - auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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] - auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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] - auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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] - auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/multipleAlign/../alignment/Alignment.h:38, - from clustalW/multipleAlign/Iteration.h:8, - from clustalW/multipleAlign/Iteration.cpp:13: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, @@ -3530,19 +3463,6 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': -clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] - int count; - ^~~~~ -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] - int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 - ^~~~~~~~~~~~~~ -clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::seqsAlignToProfile(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, int, std::__cxx11::string)': -clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] - string phylipName) - ~~~~~~~^~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, @@ -3554,6 +3474,10 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, clustalw::AlignmentSteps*, int)': +clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] + int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 + ^~~~~~~~~~~~~~ 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, @@ -3566,10 +3490,10 @@ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] - tmpnam (buffer); - ~~~~~~~^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp +clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::seqsAlignToProfile(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, int, std::__cxx11::string)': +clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] + string phylipName) + ~~~~~~~^~~~~~~~~~ In file included from clustalW/interface/../Clustal.h:18, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: @@ -3706,17 +3630,112 @@ ^~~~~~~~~ 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/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] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp +In file included from clustalW/multipleAlign/Iteration.cpp:17: +clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + 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] + auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + 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] + auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + 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] + auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + 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] + auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + 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] + auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + 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] + auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/multipleAlign/../alignment/Alignment.h:38, + from clustalW/multipleAlign/Iteration.h:8, + from clustalW/multipleAlign/Iteration.cpp:13: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp +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] + int count; + ^~~~~ 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=] clustalObj->getHelp('C'); @@ -3728,6 +3747,7 @@ clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(lin1.c_str()); ~~~~~~^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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/ProfileStandard.h:9, @@ -3738,15 +3758,18 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp +clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] + tmpnam (buffer); + ~~~~~~~^~~~~~~~ +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: +clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp @@ -3760,6 +3783,13 @@ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15: +clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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] + 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, @@ -3771,15 +3801,6 @@ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.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, @@ -3790,21 +3811,6 @@ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] - void SubMatrix::tempInterface(int alignResidueType, int alignType) - ~~~~^~~~~~~~~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.cpp:1613:57: warning: unused parameter 'alignType' [-Wunused-parameter] - void SubMatrix::tempInterface(int alignResidueType, int alignType) - ~~~~^~~~~~~~~ -clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])': -clustalW/substitutionMatrix/SubMatrix.cpp:1657:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] - int maxRes; - ^~~~~~ -clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])': -clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] - int maxRes; - ^~~~~~ 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] @@ -3826,8 +3832,8 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)': clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; @@ -3835,10 +3841,34 @@ clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp +clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::tempInterface(int, int)': +clustalW/substitutionMatrix/SubMatrix.cpp:1613:35: warning: unused parameter 'alignResidueType' [-Wunused-parameter] + void SubMatrix::tempInterface(int alignResidueType, int alignType) + ~~~~^~~~~~~~~~~~~~~~ +clustalW/substitutionMatrix/SubMatrix.cpp:1613:57: warning: unused parameter 'alignType' [-Wunused-parameter] + void SubMatrix::tempInterface(int alignResidueType, int alignType) + ~~~~^~~~~~~~~ +clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])': +clustalW/substitutionMatrix/SubMatrix.cpp:1657:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] + int maxRes; + ^~~~~~ +clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])': +clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] + int maxRes; + ^~~~~~ +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] + 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] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTreeOutput.h:11, @@ -3849,60 +3879,29 @@ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.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] + return (maxRes); + ^ 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: + from clustalW/tree/TreeInterface.h:19, + from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -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] - auto_ptr createSets(int firstSeq, int lastSeq); - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/tree/../alignment/Alignment.h:38, - from clustalW/tree/Tree.h:13, - from clustalW/tree/Tree.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -clustalW/tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr Tree::createSets(int firstSeq, int lastSeq) - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/tree/../alignment/Alignment.h:38, - from clustalW/tree/Tree.h:13, - from clustalW/tree/Tree.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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] - auto_ptr progAlignSteps; - ^~~~~~~~ -In file included from /usr/include/c++/8/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from clustalW/tree/../alignment/Alignment.h:38, - from clustalW/tree/Tree.h:13, - from clustalW/tree/Tree.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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/TreeInterface.h:19, - from clustalW/tree/TreeInterface.cpp:15: + 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] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ @@ -3979,6 +3978,7 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp In file included from clustalW/tree/ClusterTree.h:23, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/TreeInterface.cpp:17: @@ -4040,6 +4040,19 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here 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] + auto_ptr createSets(int firstSeq, int lastSeq); + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/tree/../alignment/Alignment.h:38, + from clustalW/tree/Tree.h:13, + from clustalW/tree/Tree.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ clustalW/tree/TreeInterface.cpp:195:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ @@ -4139,57 +4152,34 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here 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/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] - 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] - 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] - std::auto_ptr file; - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from clustalW/tree/ClusterTree.h:16, - from clustalW/tree/UnRootedClusterTree.h:8, - from clustalW/tree/UnRootedClusterTree.cpp:9: +clustalW/tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr Tree::createSets(int firstSeq, int lastSeq) + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/tree/../alignment/Alignment.h:38, + from clustalW/tree/Tree.h:13, + from clustalW/tree/Tree.cpp:10: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here 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] - auto_ptr quickDistMat; - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from clustalW/tree/ClusterTree.h:16, - from clustalW/tree/UnRootedClusterTree.h:8, - from clustalW/tree/UnRootedClusterTree.cpp:9: +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] + auto_ptr progAlignSteps; + ^~~~~~~~ +In file included from /usr/include/c++/8/bits/locale_conv.h:41, + from /usr/include/c++/8/locale:43, + from /usr/include/c++/8/iomanip:43, + from clustalW/tree/../alignment/Alignment.h:38, + from clustalW/tree/Tree.h:13, + from clustalW/tree/Tree.cpp:10: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, - from clustalW/tree/UPGMA/RootedGuideTree.h:17, - from clustalW/tree/UPGMA/RootedGuideTree.cpp:10: -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printInFormat(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - return (maxRes); - ^ g++ -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -dM -E -o moc_predefs.h /usr/lib/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/../ClusterTree.h:20, @@ -4201,7 +4191,6 @@ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp In file included from clustalW/tree/UPGMA/../ClusterTree.h:23, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: @@ -4227,17 +4216,6 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, - from clustalW/tree/UPGMA/RootedGuideTree.h:17, - from clustalW/tree/UPGMA/RootedTreeOutput.h:15, - from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printInFormat(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, @@ -4249,7 +4227,6 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here 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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11: clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTree(RootedGuideTree* phyTree, @@ -4293,6 +4270,65 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here 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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp +In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, + from clustalW/tree/UPGMA/RootedGuideTree.h:17, + from clustalW/tree/UPGMA/RootedTreeOutput.h:15, + from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: +clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printInFormat(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, + from clustalW/tree/UPGMA/RootedGuideTree.h:17, + from clustalW/tree/UPGMA/RootedGuideTree.cpp:10: +clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printInFormat(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.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] + 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] + 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] + std::auto_ptr file; + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from clustalW/tree/ClusterTree.h:16, + from clustalW/tree/UnRootedClusterTree.h:8, + from clustalW/tree/UnRootedClusterTree.cpp:9: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + 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] + auto_ptr quickDistMat; + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from clustalW/tree/ClusterTree.h:16, + from clustalW/tree/UnRootedClusterTree.h:8, + from clustalW/tree/UnRootedClusterTree.cpp:9: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, @@ -4304,10 +4340,7 @@ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.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] auto_ptr generateTree(RootedGuideTree* phyTree, @@ -4349,6 +4382,7 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here 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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/8 -I/usr/include/x86_64-linux-gnu/c++/8 -I/usr/include/c++/8/backward -I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include FileDialog.h -o moc_FileDialog.cpp @@ -4375,87 +4409,23 @@ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from AlignmentViewerWidget.h:36, - from moc_AlignmentViewerWidget.cpp:9: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from BootstrapTreeDialog.h:11, - from moc_BootstrapTreeDialog.cpp:9: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -In file included from moc_BootstrapTreeDialog.cpp:9: -BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr treeFileNames; - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from BootstrapTreeDialog.h:10, - from moc_BootstrapTreeDialog.cpp:9: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - 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 HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from ColorFileXmlParser.h:9, - from moc_ColorFileXmlParser.cpp:9: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from ClustalQtParams.h:13, - from HardCodedColorScheme.h:8, - from ColorParameters.h:11, - from PSPrinter.h:11, - from moc_PSPrinter.cpp:9: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from AlignmentWidget.h:41, - from moc_AlignmentWidget.cpp:9: + from AlignmentViewerWidget.h:36, + from moc_AlignmentViewerWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, @@ -4467,6 +4437,7 @@ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp In file included from moc_AlignOutputFileNames.cpp:9: AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr outFileNames; @@ -4480,18 +4451,28 @@ 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:9: + from BootstrapTreeDialog.h:11, + from moc_BootstrapTreeDialog.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +In file included from moc_BootstrapTreeDialog.cpp:9: +BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr treeFileNames; + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from BootstrapTreeDialog.h:10, + from moc_BootstrapTreeDialog.cpp:9: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, - from SeqNameWidget.h:41, - from moc_SeqNameWidget.cpp:9: + from AlignmentWidget.h:41, + from moc_AlignmentWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ @@ -4500,68 +4481,45 @@ ^~~~~~~~~~~~~~ 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:9: + from AlignmentViewerWidget.h:36, + from mainwindow.h:37, + from moc_mainwindow.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-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 ClustalQtParams.h:13, - from WritePostscriptFile.h:10, - from moc_WritePostscriptFile.cpp:9: + from HardCodedColorScheme.h:8, + from ColorParameters.h:11, + from ColorFileXmlParser.h:9, + from moc_ColorFileXmlParser.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, - from TreeOutputFileNames.h:10, - from moc_TreeOutputFileNames.cpp:9: -clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 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] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -In file included from moc_WritePostscriptFile.cpp:9: -WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr params; - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from WritePostscriptFile.h:9, - from moc_WritePostscriptFile.cpp:9: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from moc_TreeOutputFileNames.cpp:9: -TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr treeFileNames; - ^~~~~~~~ -In file included from /usr/include/c++/8/memory:80, - from TreeOutputFileNames.h:9, - from moc_TreeOutputFileNames.cpp:9: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, - from clustalW/alignment/Alignment.h:42, - from AlignmentViewerWidget.h:36, - from mainwindow.h:37, - from moc_mainwindow.cpp:9: + from HelpDisplayWidget.h:18, + from moc_HelpDisplayWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp +g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp In file included from clustalW/Clustal.h:18, from mainwindow.h:45, from moc_mainwindow.cpp:9: @@ -4722,6 +4680,82 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here 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 HardCodedColorScheme.h:8, + from ColorParameters.h:11, + from PSPrinter.h:11, + from moc_PSPrinter.cpp:9: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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] + 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:9: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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] + 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:9: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from TreeOutputFileNames.h:10, + from moc_TreeOutputFileNames.cpp:9: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +In file included from moc_TreeOutputFileNames.cpp:9: +TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr treeFileNames; + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from TreeOutputFileNames.h:9, + from moc_TreeOutputFileNames.cpp:9: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, + from clustalW/alignment/Alignment.h:42, + from ClustalQtParams.h:13, + from WritePostscriptFile.h:10, + from moc_WritePostscriptFile.cpp:9: +clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +In file included from moc_WritePostscriptFile.cpp:9: +WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr params; + ^~~~~~~~ +In file included from /usr/include/c++/8/memory:80, + from WritePostscriptFile.h:9, + from moc_WritePostscriptFile.cpp:9: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o -lQt5Widgets -lQt5Gui -lQt5Xml -lQt5Core -lGL -lpthread /usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./clustalW/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp' @@ -4755,20 +4789,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-8_amd64.deb'. dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-8_amd64.deb'. +dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-8_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../clustalx_2.1+lgpl-8_amd64.changes 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/61328/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/61328/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/53490 and its subdirectories -I: Current time: Fri Aug 5 11:05:28 -12 2022 -I: pbuilder-time-stamp: 1659740728 +I: removing directory /srv/workspace/pbuilder/61328 and its subdirectories +I: Current time: Sun Jul 4 06:44:00 +14 2021 +I: pbuilder-time-stamp: 1625330640