Diff of the two buildlogs: -- --- b1/build.log 2021-08-24 11:45:40.984921597 +0000 +++ b2/build.log 2021-08-24 11:46:30.023080740 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 26 06:05:23 -12 2022 -I: pbuilder-time-stamp: 1664215523 +I: Current time: Wed Aug 25 01:45:42 +14 2021 +I: pbuilder-time-stamp: 1629805542 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 Sat Jul 14 03:12:38 2018 -12 +gpgv: Signature made Sun Jul 15 05:12:38 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,136 +29,170 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/82741/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1006196/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/1006196/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1006196/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='c0417706c40b4504a70822b1d95402e9' - 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='82741' - PS1='# ' - PS2='> ' + INVOCATION_ID=2dafbc3a96f44559881aaeb2fb6d509e + 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=1006196 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.pFRVlbZP2D/pbuilderrc_XtXV --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.pFRVlbZP2D/b1 --logfile b1/build.log clustalw_2.1+lgpl-6.dsc' - SUDO_GID='110' - SUDO_UID='105' - 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.pFRVlbZP2D/pbuilderrc_OOFB --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.pFRVlbZP2D/b2 --logfile b2/build.log clustalw_2.1+lgpl-6.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 ionos5-amd64 5.10.0-8-amd64 #1 SMP Debian 5.10.46-4 (2021-08-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-amd64 #1 SMP Debian 5.10.46-4 (2021-08-03) 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 Sep 9 02:46 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/82741/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 Aug 25 01:45 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 7 22:25 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/1006196/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +261,7 @@ Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] -Fetched 19.0 MB in 1s (27.4 MB/s) +Fetched 19.0 MB in 0s (70.9 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.) @@ -382,7 +416,8 @@ 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/clustalw-2.1+lgpl/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../clustalw_2.1+lgpl-6_source.changes +hostname: Name or service not known +I: Running cd /build/clustalw-2.1+lgpl/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../clustalw_2.1+lgpl-6_source.changes dpkg-buildpackage: info: source package clustalw dpkg-buildpackage: info: source version 2.1+lgpl-6 dpkg-buildpackage: info: source distribution unstable @@ -569,7 +604,7 @@ config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build - make -j16 + make -j15 make[1]: Entering directory '/build/clustalw-2.1+lgpl' Making all in m4 make[2]: Entering directory '/build/clustalw-2.1+lgpl/m4' @@ -595,17 +630,6 @@ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp -In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./tree/UPGMA/../../alignment/Alignment.h:42, - from ./tree/UPGMA/RootedGuideTree.h:17, - from ./tree/UPGMA/RootedGuideTree.cpp:10: -./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"); - ^~~~~~~~~~~~~~ -./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 ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, @@ -617,29 +641,37 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp -In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./tree/UPGMA/../../alignment/Alignment.h:42, - from ./tree/UPGMA/../ClusterTree.h:20, - from ./tree/UPGMA/RootedClusterTree.h:8, - from ./tree/UPGMA/RootedClusterTree.cpp:9: -./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./fileInput/../alignment/Alignment.h:42, + from ./fileInput/FileReader.h:12, + from ./fileInput/FileReader.cpp:29: +./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"); ^~~~~~~~~~~~~~ -./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +./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 ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, - from ./tree/UPGMA/RootedGuideTree.h:17, - from ./tree/UPGMA/UPGMAAlgorithm.h:8, - from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: + from ./tree/UPGMA/../ClusterTree.h:20, + from ./tree/UPGMA/RootedClusterTree.h:8, + from ./tree/UPGMA/RootedClusterTree.cpp:9: ./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"); ^~~~~~~~~~~~~~ ./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 ./fileInput/FileReader.cpp:29: +./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 ./fileInput/FileReader.h:11, + from ./fileInput/FileReader.cpp:29: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ In file included from ./tree/UPGMA/../ClusterTree.h:23, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: @@ -665,27 +697,26 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./pairwise/../alignment/Alignment.h:42, - from ./pairwise/PairwiseAlignBase.h:10, - from ./pairwise/FullPairwiseAlign.h:9, - from ./pairwise/FullPairwiseAlign.cpp:9: -./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"); - ^~~~~~~~~~~~~~ -./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"); - ^~~~~~~~~~~~~~ -In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./fileInput/../alignment/Alignment.h:42, - from ./fileInput/FileReader.h:12, +./fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::__cxx11::string*)': +./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 ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: -./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"); - ^~~~~~~~~~~~~~ -./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"); - ^~~~~~~~~~~~~~ +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +./fileInput/FileReader.cpp: At global scope: +./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 ./fileInput/FileReader.h:11, + from ./fileInput/FileReader.cpp:29: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, @@ -740,6 +771,31 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./pairwise/../alignment/Alignment.h:42, + from ./pairwise/PairwiseAlignBase.h:10, + from ./pairwise/FullPairwiseAlign.h:9, + from ./pairwise/FullPairwiseAlign.cpp:9: +./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"); + ^~~~~~~~~~~~~~ +./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp +In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./tree/UPGMA/../../alignment/Alignment.h:42, + from ./tree/UPGMA/RootedGuideTree.h:17, + from ./tree/UPGMA/UPGMAAlgorithm.h:8, + from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: +./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"); + ^~~~~~~~~~~~~~ +./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 ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTree(RootedGuideTree* phyTree, @@ -781,39 +837,19 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -In file included from ./fileInput/FileReader.cpp:29: -./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 ./fileInput/FileReader.h:11, - from ./fileInput/FileReader.cpp:29: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -./fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::__cxx11::string*)': -./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 ./fileInput/FileReader.h:11, - from ./fileInput/FileReader.cpp:29: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -./fileInput/FileReader.cpp: At global scope: -./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 ./fileInput/FileReader.h:11, - from ./fileInput/FileReader.cpp:29: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp +In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./tree/UPGMA/../../alignment/Alignment.h:42, + from ./tree/UPGMA/RootedGuideTree.h:17, + from ./tree/UPGMA/RootedGuideTree.cpp:10: +./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"); + ^~~~~~~~~~~~~~ +./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"); + ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, @@ -825,6 +861,11 @@ ./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"); ^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/Tree.h:13, @@ -835,9 +876,7 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp In file included from ./tree/Tree.cpp:10: ./tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr createSets(int firstSeq, int lastSeq); @@ -876,9 +915,10 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, @@ -889,7 +929,6 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp In file included from ./tree/ClusterTree.h:23, from ./tree/ClusterTree.cpp:9: ./tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -911,8 +950,17 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp +In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./tree/../alignment/Alignment.h:42, + from ./tree/ClusterTree.h:20, + from ./tree/UnRootedClusterTree.h:8, + from ./tree/UnRootedClusterTree.cpp:9: +./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printInFormat(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/TreeInterface.h:19, @@ -923,6 +971,31 @@ ./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 ./tree/ClusterTree.h:23, + from ./tree/UnRootedClusterTree.h:8, + from ./tree/UnRootedClusterTree.cpp:9: +./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 ./tree/ClusterTree.h:16, + from ./tree/UnRootedClusterTree.h:8, + from ./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 ./tree/UnRootedClusterTree.h:8, + from ./tree/UnRootedClusterTree.cpp:9: +./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 ./tree/ClusterTree.h:16, + from ./tree/UnRootedClusterTree.h:8, + from ./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 ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, @@ -993,8 +1066,7 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp In file included from ./tree/ClusterTree.h:23, from ./tree/UnRootedClusterTree.h:8, from ./tree/TreeInterface.cpp:17: @@ -1028,6 +1100,16 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./tree/../alignment/Alignment.h:42, + from ./tree/ClusterTreeOutput.h:11, + from ./tree/ClusterTreeOutput.cpp:9: +./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"); + ^~~~~~~~~~~~~~ +./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 ./tree/TreeInterface.cpp:23: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, @@ -1155,156 +1237,7 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp -In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./multipleAlign/../alignment/Alignment.h:42, - from ./multipleAlign/Iteration.h:8, - from ./multipleAlign/Iteration.cpp:13: -./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"); - ^~~~~~~~~~~~~~ -./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp -In file included from ./multipleAlign/Iteration.cpp:17: -./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 ./multipleAlign/../alignment/Alignment.h:38, - from ./multipleAlign/Iteration.h:8, - from ./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 ./multipleAlign/Iteration.cpp:17: -./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 ./multipleAlign/../alignment/Alignment.h:38, - from ./multipleAlign/Iteration.h:8, - from ./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 ./multipleAlign/Iteration.cpp:17: -./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 ./multipleAlign/../alignment/Alignment.h:38, - from ./multipleAlign/Iteration.h:8, - from ./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 ./multipleAlign/Iteration.cpp:17: -./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 ./multipleAlign/../alignment/Alignment.h:38, - from ./multipleAlign/Iteration.h:8, - from ./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 ./multipleAlign/Iteration.cpp:17: -./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 ./multipleAlign/../alignment/Alignment.h:38, - from ./multipleAlign/Iteration.h:8, - from ./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 ./multipleAlign/Iteration.cpp:17: -./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 ./multipleAlign/../alignment/Alignment.h:38, - from ./multipleAlign/Iteration.h:8, - from ./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 ./multipleAlign/Iteration.cpp:17: -./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 ./multipleAlign/../alignment/Alignment.h:38, - from ./multipleAlign/Iteration.h:8, - from ./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 ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./tree/../alignment/Alignment.h:42, - from ./tree/ClusterTree.h:20, - from ./tree/UnRootedClusterTree.h:8, - from ./tree/UnRootedClusterTree.cpp:9: -./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printInFormat(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -In file included from ./tree/ClusterTree.h:23, - from ./tree/UnRootedClusterTree.h:8, - from ./tree/UnRootedClusterTree.cpp:9: -./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 ./tree/ClusterTree.h:16, - from ./tree/UnRootedClusterTree.h:8, - from ./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 ./tree/UnRootedClusterTree.h:8, - from ./tree/UnRootedClusterTree.cpp:9: -./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 ./tree/ClusterTree.h:16, - from ./tree/UnRootedClusterTree.h:8, - from ./tree/UnRootedClusterTree.cpp:9: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -./multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': -./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] - tmpnam (buffer); - ~~~~~~~^~~~~~~~ -In file included from ./substitutionMatrix/SubMatrix.cpp:15: -./substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printInFormat(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -./substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, @@ -1317,16 +1250,11 @@ ./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"); ^~~~~~~~~~~~~~ -In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./interface/../fileInput/../alignment/Alignment.h:42, - from ./interface/../fileInput/FileReader.h:12, - from ./interface/../Clustal.h:18, - from ./interface/CommandLineParser.h:18, - from ./interface/CommandLineParser.cpp:13: -./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +In file included from ./substitutionMatrix/SubMatrix.cpp:15: +./substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ -./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] +./substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./interface/../Clustal.h:18, @@ -1420,12 +1348,23 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./multipleAlign/../alignment/Alignment.h:42, + from ./multipleAlign/ProfileBase.h:14, + from ./multipleAlign/MSA.h:10, + from ./multipleAlign/MSA.cpp:16: +./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"); + ^~~~~~~~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ +./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 /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, @@ -1459,6 +1398,131 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./multipleAlign/../alignment/Alignment.h:42, + from ./multipleAlign/Iteration.h:8, + from ./multipleAlign/Iteration.cpp:13: +./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"); + ^~~~~~~~~~~~~~ +./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 ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./multipleAlign/../alignment/Alignment.h:42, + from ./multipleAlign/ProfileAlignAlgorithm.h:10, + from ./multipleAlign/MyersMillerProfileAlign.h:10, + from ./multipleAlign/MyersMillerProfileAlign.cpp:10: +./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printInFormat(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +In file included from ./multipleAlign/Iteration.cpp:17: +./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 ./multipleAlign/../alignment/Alignment.h:38, + from ./multipleAlign/Iteration.h:8, + from ./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 ./multipleAlign/Iteration.cpp:17: +./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 ./multipleAlign/../alignment/Alignment.h:38, + from ./multipleAlign/Iteration.h:8, + from ./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 ./multipleAlign/Iteration.cpp:17: +./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 ./multipleAlign/../alignment/Alignment.h:38, + from ./multipleAlign/Iteration.h:8, + from ./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 ./multipleAlign/Iteration.cpp:17: +./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 ./multipleAlign/../alignment/Alignment.h:38, + from ./multipleAlign/Iteration.h:8, + from ./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 ./multipleAlign/Iteration.cpp:17: +./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 ./multipleAlign/../alignment/Alignment.h:38, + from ./multipleAlign/Iteration.h:8, + from ./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 ./multipleAlign/Iteration.cpp:17: +./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 ./multipleAlign/../alignment/Alignment.h:38, + from ./multipleAlign/Iteration.h:8, + from ./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 ./multipleAlign/Iteration.cpp:17: +./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 ./multipleAlign/../alignment/Alignment.h:38, + from ./multipleAlign/Iteration.h:8, + from ./multipleAlign/Iteration.cpp:13: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp +In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./interface/../fileInput/../alignment/Alignment.h:42, + from ./interface/../fileInput/FileReader.h:12, + from ./interface/../Clustal.h:18, + from ./interface/CommandLineParser.h:18, + from ./interface/CommandLineParser.cpp:13: +./interface/../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"); + ^~~~~~~~~~~~~~ +./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"); + ^~~~~~~~~~~~~~ In file included from ./interface/../Clustal.h:18, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: @@ -1629,38 +1693,10 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./multipleAlign/../alignment/Alignment.h:42, - from ./multipleAlign/ProfileBase.h:14, - from ./multipleAlign/MSA.h:10, - from ./multipleAlign/MSA.cpp:16: -./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"); - ^~~~~~~~~~~~~~ -./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 ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./tree/../alignment/Alignment.h:42, - from ./tree/ClusterTreeOutput.h:11, - from ./tree/ClusterTreeOutput.cpp:9: -./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"); - ^~~~~~~~~~~~~~ -./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 ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./multipleAlign/../alignment/Alignment.h:42, - from ./multipleAlign/ProfileAlignAlgorithm.h:10, - from ./multipleAlign/MyersMillerProfileAlign.h:10, - from ./multipleAlign/MyersMillerProfileAlign.cpp:10: -./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printInFormat(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ +./interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': +./interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system(lin1.c_str()); + ~~~~~~^~~~~~~~~~~~~~ In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileStandard.h:9, @@ -1671,12 +1707,10 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp -./interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': -./interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system(lin1.c_str()); - ~~~~~~^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp +./multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': +./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] + tmpnam (buffer); + ~~~~~~~^~~~~~~~ In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileWithSub.h:9, @@ -1687,10 +1721,11 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, - from ./multipleAlign/LowScoreSegProfile.h:13, - from ./multipleAlign/LowScoreSegProfile.cpp:9: + from ./multipleAlign/ProfileBase.h:14, + from ./multipleAlign/ProfileBase.cpp:9: ./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"); ^~~~~~~~~~~~~~ @@ -1698,22 +1733,20 @@ void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, - from ./multipleAlign/ProfileBase.h:14, - from ./multipleAlign/ProfileBase.cpp:9: + from ./multipleAlign/LowScoreSegProfile.h:13, + from ./multipleAlign/LowScoreSegProfile.cpp:9: ./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"); ^~~~~~~~~~~~~~ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp In file included from ./general/OutputFile.cpp:9: ./general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; @@ -1724,8 +1757,11 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp ./general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)': ./general/Utility.cpp:183:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); @@ -1734,7 +1770,6 @@ ./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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp @@ -1770,15 +1805,6 @@ ^~~~~~~~~~~~~~ In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, - from ./main.cpp:10: -./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printInFormat(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - void printVectorToFile(vector& temp, char* name = "tempfile.out"); - ^~~~~~~~~~~~~~ -In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, - from ./alignment/Alignment.h:42, from ./alignment/AlignmentOutput.h:24, from ./alignment/AlignmentOutput.cpp:27: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -1877,6 +1903,17 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, + from ./fileInput/../alignment/Alignment.h:42, + from ./fileInput/FileReader.h:12, + from ./Clustal.h:18, + from ./Clustal.cpp:27: +./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"); + ^~~~~~~~~~~~~~ +./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"); + ^~~~~~~~~~~~~~ ./alignment/AlignmentOutput.cpp:512:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) ^~~~~~~~ @@ -1895,155 +1932,6 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -In file included from ./main.cpp:16: -./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/bits/locale_conv.h:41, - from /usr/include/c++/8/locale:43, - from /usr/include/c++/8/iomanip:43, - from ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - bool openExplicitFile(auto_ptr& outFile, string fileName); - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - string openOutputFile(auto_ptr& outFile, string prompt, string path, - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr clustalOutFile; - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr gcgOutFile; - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr nbrfOutFile; - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr phylipOutFile; - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr gdeOutFile; - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr nexusOutFile; - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./interface/../Clustal.h:20, - from ./interface/InteractiveMenu.h:15, - from ./main.cpp:17: -./interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - auto_ptr fastaOutFile; - ^~~~~~~~ -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 ./alignment/Alignment.h:38, - from ./main.cpp:10: -/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here - template class auto_ptr; - ^~~~~~~~ -In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, - from ./fileInput/../alignment/Alignment.h:42, - from ./fileInput/FileReader.h:12, - from ./Clustal.h:18, - from ./Clustal.cpp:27: -./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"); - ^~~~~~~~~~~~~~ -./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 ./Clustal.h:18, from ./Clustal.cpp:27: ./fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -2320,6 +2208,153 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ +In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, + from ./alignment/Alignment.h:42, + from ./main.cpp:10: +./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printInFormat(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + void printVectorToFile(vector& temp, char* name = "tempfile.out"); + ^~~~~~~~~~~~~~ +In file included from ./main.cpp:16: +./fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + void checkInfile(int* nseqs, auto_ptr& fileParser); + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + bool openExplicitFile(auto_ptr& outFile, string fileName); + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + string openOutputFile(auto_ptr& outFile, string prompt, string path, + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr clustalOutFile; + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr gcgOutFile; + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr nbrfOutFile; + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr phylipOutFile; + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr gdeOutFile; + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr nexusOutFile; + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ +In file included from ./interface/../Clustal.h:20, + from ./interface/InteractiveMenu.h:15, + from ./main.cpp:17: +./interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + auto_ptr fastaOutFile; + ^~~~~~~~ +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 ./alignment/Alignment.h:38, + from ./main.cpp:10: +/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here + template class auto_ptr; + ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalw2 FullPairwiseAlign.o FastPairwiseAlign.o MSFFileParser.o FileReader.o PIRFileParser.o RSFFileParser.o GDEFileParser.o InFileStream.o ClustalFileParser.o PearsonFileParser.o FileParser.o EMBLFileParser.o RootedClusterTree.o UPGMAAlgorithm.o Node.o RootedGuideTree.o RootedTreeOutput.o Tree.o ClusterTree.o TreeInterface.o UnRootedClusterTree.o ClusterTreeOutput.o RandomGenerator.o NJTree.o AlignmentSteps.o InteractiveMenu.o CommandLineParser.o SubMatrix.o Iteration.o MSA.o MyersMillerProfileAlign.o ProfileStandard.o ProfileWithSub.o ProfileBase.o LowScoreSegProfile.o OutputFile.o UserParameters.o Utility.o InvalidCombination.o DebugLog.o ClustalWResources.o VectorOutOfRange.o SymMatrix.o Stats.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o Clustal.o main.o /usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./src/./multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp' @@ -2331,7 +2366,7 @@ make[2]: Leaving directory '/build/clustalw-2.1+lgpl' make[1]: Leaving directory '/build/clustalw-2.1+lgpl' dh_auto_test - make -j16 check VERBOSE=1 + make -j15 check VERBOSE=1 make[1]: Entering directory '/build/clustalw-2.1+lgpl' Making check in m4 make[2]: Entering directory '/build/clustalw-2.1+lgpl/m4' @@ -2352,7 +2387,7 @@ dh_testroot dh_prep dh_auto_install - make -j16 install DESTDIR=/build/clustalw-2.1\+lgpl/debian/clustalw AM_UPDATE_INFO_DIR=no + make -j15 install DESTDIR=/build/clustalw-2.1\+lgpl/debian/clustalw AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/clustalw-2.1+lgpl' Making install in m4 make[2]: Entering directory '/build/clustalw-2.1+lgpl/m4' @@ -2413,12 +2448,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1006196/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1006196/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/82741 and its subdirectories -I: Current time: Mon Sep 26 06:08:40 -12 2022 -I: pbuilder-time-stamp: 1664215720 +I: removing directory /srv/workspace/pbuilder/1006196 and its subdirectories +I: Current time: Wed Aug 25 01:46:29 +14 2021 +I: pbuilder-time-stamp: 1629805589