Tue Jul 28 02:23:16 UTC 2020 I: starting to build clustalw/buster/i386 on jenkins on '2020-07-28 02:23' Tue Jul 28 02:23:16 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/9850/console.log Tue Jul 28 02:23:16 UTC 2020 I: Downloading source for buster/clustalw=2.1+lgpl-6 --2020-07-28 02:23:16-- http://deb.debian.org/debian/pool/main/c/clustalw/clustalw_2.1+lgpl-6.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2050 (2.0K) Saving to: ‘clustalw_2.1+lgpl-6.dsc’ 0K .. 100% 10.8M=0s 2020-07-28 02:23:16 (10.8 MB/s) - ‘clustalw_2.1+lgpl-6.dsc’ saved [2050/2050] Tue Jul 28 02:23:16 UTC 2020 I: clustalw_2.1+lgpl-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: clustalw Binary: clustalw Architecture: any Version: 2.1+lgpl-6 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: http://www.clustal.org/clustal2/ Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/clustalw Vcs-Git: https://salsa.debian.org/med-team/clustalw.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~) Package-List: clustalw deb science optional arch=any Checksums-Sha1: f29784f68585544baa77cbeca6392e533d4cf433 350761 clustalw_2.1+lgpl.orig.tar.gz caa96d12fe4806f93574ecfd5f8428a1058f8cc2 19920 clustalw_2.1+lgpl-6.debian.tar.xz Checksums-Sha256: e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486 350761 clustalw_2.1+lgpl.orig.tar.gz 733ee21257189705234d10a61cf9db72028bcae49e0fe959f363464165032403 19920 clustalw_2.1+lgpl-6.debian.tar.xz Files: 144df8440a0ae083d5167616c8ceeb41 350761 clustalw_2.1+lgpl.orig.tar.gz 29fbeb5aa513189a9141eaf0f9b09c5b 19920 clustalw_2.1+lgpl-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAltKEuYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEAYQ/8DVO/41RpBvzqAwxGBZeFN5isOSTz0O1A RY9rzpbI8dJy6vppVoTLEL0arcV89R3mAvNwyA6p8G5+8uHcBOBcHWY5g7BcaP/R muexNVqUlxioJrnPZG5QdqyA82CzTm58318VB8Su1GeWoZqZ055chU0OSZQ+Ms0O jWnETPdMqpzGHBhyIcPGgbI77XbDFCyMl7b1nqyqRs6uO8Uw+S6zNLEKYJZhWW3g dqvzRvUmJnzB/+nz53AW2Qh0WZ9rY7f4fqJDXDWa20L/JpnXkncqFHrvjkk0B1Do GTFQzfqbQE2jZL/33PMAYVFWitM0rl86XDSyq5e4ZiLvvip6yCqE1U7Ezv2c/cwt TTWFUzjEFqi5lfTBBBM9aHxDD3RV/r4JzL4TFyqpYno3v1+/rFhGZtsb2l20oRzP ZFFrCfOxx4wchGonRuxS2zvN4d+UM2bk+kQ8tShh44JecNm5jFRXxms1ixSro+Ii Avs+bkoBxVtFFHZHlOLgHLR8G9F3h9VD7K4Ajsw27+r6THL93ESP2AljkzU2ngaP lQvm6VsdmCdsrOL7TdnUVBPBrUfMgrirAX9DOO6UBjsogN8op6SyE7Bv8znmPr1D 59Mx1eMyltYiBfc5rw4mduRFnC3qtPrTXu7kNeidSBt7DCqBqAj5WLZClGIO+9H7 4gj0buNKVqc= =OVB/ -----END PGP SIGNATURE----- Tue Jul 28 02:23:16 UTC 2020 I: Checking whether the package is not for us Tue Jul 28 02:23:16 UTC 2020 I: Starting 1st build on remote node profitbricks-build2-i386.debian.net. Tue Jul 28 02:23:16 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build2-i386.debian.net. Tue Jul 28 02:26:54 UTC 2020 I: Deleting $TMPDIR on profitbricks-build2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 27 14:23:18 -12 2020 I: pbuilder-time-stamp: 1595902998 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [clustalw_2.1+lgpl-6.dsc] I: copying [./clustalw_2.1+lgpl.orig.tar.gz] I: copying [./clustalw_2.1+lgpl-6.debian.tar.xz] 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: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./clustalw_2.1+lgpl-6.dsc dpkg-source: info: extracting clustalw in clustalw-2.1+lgpl dpkg-source: info: unpacking clustalw_2.1+lgpl.orig.tar.gz dpkg-source: info: unpacking clustalw_2.1+lgpl-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30791/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='41256decd4294507a334e2633658ecb4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='30791' PS1='# ' PS2='> ' 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.9nmKY62VF2/pbuilderrc_Pgyq --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9nmKY62VF2/b1 --logfile b1/build.log clustalw_2.1+lgpl-6.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux profitbricks-build2-i386 4.19.0-9-686-pae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) i686 GNU/Linux I: ls -l /bin total 5488 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 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 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 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 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 206392 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 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 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 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 26 21:17 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 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/30791/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19234 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 70.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Fetched 19.4 MB in 3s (6037 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_i386.deb ... Unpacking libicu63:i386 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../27-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... 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Reading state information... 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 dpkg-buildpackage: info: source package clustalw dpkg-buildpackage: info: source version 2.1+lgpl-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf configure.ac:79: installing './compile' src/Makefile.am:21: warning: source file './pairwise/FullPairwiseAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am:21: warning: source file './pairwise/FastPairwiseAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/MSFFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/FileReader.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/PIRFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/RSFFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/GDEFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/InFileStream.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/ClustalFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/PearsonFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/FileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/EMBLFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/UPGMAAlgorithm.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/Node.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedGuideTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedTreeOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/Tree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/ClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/TreeInterface.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UnRootedClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/ClusterTreeOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/RandomGenerator.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/NJTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/AlignmentSteps.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './interface/InteractiveMenu.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './interface/CommandLineParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './substitutionMatrix/SubMatrix.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/Iteration.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/MSA.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/MyersMillerProfileAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileStandard.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileWithSub.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileBase.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/LowScoreSegProfile.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/OutputFile.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/UserParameters.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/Utility.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/InvalidCombination.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/DebugLog.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/ClustalWResources.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/VectorOutOfRange.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/SymMatrix.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/Stats.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './Help.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/Alignment.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/AlignmentOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/ObjectiveScore.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/Sequence.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './Clustal.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './main.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu building for linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make sets $(MAKE)... (cached) yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make -j10 make[1]: Entering directory '/build/clustalw-2.1+lgpl' Making all in m4 make[2]: Entering directory '/build/clustalw-2.1+lgpl/m4' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/clustalw-2.1+lgpl/m4' Making all in src make[2]: Entering directory '/build/clustalw-2.1+lgpl/src' make all-recursive make[3]: Entering directory '/build/clustalw-2.1+lgpl/src' make[4]: Entering directory '/build/clustalw-2.1+lgpl/src' 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 FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.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 FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.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 MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.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 FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.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 PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.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 RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.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 GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.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 InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.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 ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FastPairwiseAlign.h:9, from ./pairwise/FastPairwiseAlign.cpp:10: ./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 ./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, 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"); ^~~~~~~~~~~~~~ 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 FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp 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 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 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] 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/../ClusterTree.h:23, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../../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/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../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/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /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, ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /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:11: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTree(RootedGuideTree* phyTree, ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /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:11: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/UPGMA/RootedClusterTree.cpp: In member function 'std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string&)': ./tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /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/ClusterTree.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/ClusterTree.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/ClusterTree.cpp:9: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/ClusterTree.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/ClusterTree.cpp:9: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, 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, ^~~~~~~~ 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 ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ 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 ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, ^~~~~~~~ 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 ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedTreeOutput.h:15, from ./tree/UPGMA/RootedTreeOutput.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 ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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/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 ./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); ^~~~~~~~ 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 ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./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 ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/Tree.cpp: In member function 'std::auto_ptr clustalw::Tree::createSets(int, int)': ./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 ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./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 ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/TreeInterface.h:19, from ./tree/TreeInterface.cpp:15: ./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:15: ./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/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /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: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/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /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: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/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /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: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/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /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: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/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /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: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/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /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: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/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/ClusterTree.h:23, from ./tree/UnRootedClusterTree.h:8, from ./tree/TreeInterface.cpp:17: ./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/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /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/TreeInterface.cpp:17: ./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/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:18: ./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/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ 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, ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp:31:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp:103:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp:195:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': ./tree/TreeInterface.cpp:200:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:208:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::__cxx11::string*, std::vector*, int, int, bool*)': ./tree/TreeInterface.cpp:214:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:439:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::__cxx11::string*, std::vector*, int, int, bool*)': ./tree/TreeInterface.cpp:445:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:485:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': ./tree/TreeInterface.cpp:490:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:503:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs, ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': ./tree/TreeInterface.cpp:506:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /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 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 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 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; ^~~~~~~~ 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"); ^~~~~~~~~~~~~~ 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 CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp 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 ./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/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./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/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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 ./interface/InteractiveMenu.cpp:23: ./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 ./interface/InteractiveMenu.cpp:21: /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/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 ./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, 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: ./interface/../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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./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 ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /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"); ^~~~~~~~~~~~~~ ./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()); ~~~~~~^~~~~~~~~~~~~~ ./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); ~~~~~~~^~~~~~~~ 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/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"); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileStandard.h:9, from ./multipleAlign/ProfileStandard.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 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/ProfileWithSub.h:9, from ./multipleAlign/ProfileWithSub.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"); ^~~~~~~~~~~~~~ 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: ./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/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 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 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 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; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./general/OutputFile.h:8, from ./general/OutputFile.cpp:9: /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 DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.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); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ ./general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)': ./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 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 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 g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/ObjectiveScore.h:15, from ./alignment/ObjectiveScore.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 ./general/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./general/../alignment/Alignment.h:42, from ./general/Stats.cpp:15: ./general/../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"); ^~~~~~~~~~~~~~ ./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"); ^~~~~~~~~~~~~~ In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./alignment/Alignment.cpp:25: ./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 ./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 ./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 ./Clustal.h:18, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./Clustal.cpp: In member function 'void clustalw::Clustal::align(std::__cxx11::string*, bool)': ./Clustal.cpp:162:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ 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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./Clustal.cpp: In member function 'void clustalw::Clustal::doAlignUseOldTree(std::__cxx11::string*)': ./Clustal.cpp:837:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ 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 ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /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 ./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] 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/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./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/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./alignment/AlignmentOutput.cpp:512:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./alignment/AlignmentOutput.cpp:535:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string AlignmentOutput::openOutputFile(auto_ptr& outFile, string prompt, ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /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' make[4]: Leaving directory '/build/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/build/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/build/clustalw-2.1+lgpl/src' make[2]: Entering directory '/build/clustalw-2.1+lgpl' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/clustalw-2.1+lgpl' make[1]: Leaving directory '/build/clustalw-2.1+lgpl' dh_auto_test make -j10 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' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/clustalw-2.1+lgpl/m4' Making check in src make[2]: Entering directory '/build/clustalw-2.1+lgpl/src' make[3]: Entering directory '/build/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/build/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/build/clustalw-2.1+lgpl/src' make[2]: Entering directory '/build/clustalw-2.1+lgpl' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/clustalw-2.1+lgpl' make[1]: Leaving directory '/build/clustalw-2.1+lgpl' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j10 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' make[3]: Entering directory '/build/clustalw-2.1+lgpl/m4' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Leaving directory '/build/clustalw-2.1+lgpl/m4' make[2]: Leaving directory '/build/clustalw-2.1+lgpl/m4' Making install in src make[2]: Entering directory '/build/clustalw-2.1+lgpl/src' make[3]: Entering directory '/build/clustalw-2.1+lgpl/src' make[4]: Entering directory '/build/clustalw-2.1+lgpl/src' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/clustalw-2.1+lgpl/debian/clustalw/usr/bin' /usr/bin/install -c clustalw2 '/build/clustalw-2.1+lgpl/debian/clustalw/usr/bin' make[4]: Leaving directory '/build/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/build/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/build/clustalw-2.1+lgpl/src' make[2]: Entering directory '/build/clustalw-2.1+lgpl' make[3]: Entering directory '/build/clustalw-2.1+lgpl' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/clustalw-2.1+lgpl' make[2]: Leaving directory '/build/clustalw-2.1+lgpl' make[1]: Leaving directory '/build/clustalw-2.1+lgpl' debian/rules override_dh_install make[1]: Entering directory '/build/clustalw-2.1+lgpl' dh_install # We have to ask upstream if it is important for them that the binary is named clustalw2 mv /build/clustalw-2.1+lgpl/debian/clustalw/usr/bin/clustalw2 /build/clustalw-2.1+lgpl/debian/clustalw/usr/bin/clustalw make[1]: Leaving directory '/build/clustalw-2.1+lgpl' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/clustalw-2.1+lgpl' dh_installchangelogs debian/CHANGELOG.upstream make[1]: Leaving directory '/build/clustalw-2.1+lgpl' dh_installexamples dh_installman dh_installmenu dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'clustalw-dbgsym' in '../clustalw-dbgsym_2.1+lgpl-6_i386.deb'. dpkg-deb: building package 'clustalw' in '../clustalw_2.1+lgpl-6_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../clustalw_2.1+lgpl-6_i386.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: 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/30791 and its subdirectories I: Current time: Mon Jul 27 14:26:53 -12 2020 I: pbuilder-time-stamp: 1595903213 Tue Jul 28 02:26:54 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build6-i386.debian.net. Tue Jul 28 02:26:54 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build6-i386.debian.net. Tue Jul 28 02:27:30 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. Tue Jul 28 02:27:31 UTC 2020 I: clustalw_2.1+lgpl-6_i386.changes: Format: 1.8 Date: Sat, 14 Jul 2018 17:09:36 +0200 Source: clustalw Binary: clustalw clustalw-dbgsym Architecture: i386 Version: 2.1+lgpl-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: clustalw - global multiple nucleotide or peptide sequence alignment Changes: clustalw (2.1+lgpl-6) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 * d/rules: - drop now unneeded hack to remove aclocal dir - drop explicit mentioning of autotools_dev Checksums-Sha1: 79fac5682035e41d03a922ef0b859c32002566d9 4699240 clustalw-dbgsym_2.1+lgpl-6_i386.deb 7e0acd25971b2128f2bbd558c3571b7cfe6107e4 4615 clustalw_2.1+lgpl-6_i386.buildinfo b53601bd3aeb6e309b32e155e1fb43c43854738e 301408 clustalw_2.1+lgpl-6_i386.deb Checksums-Sha256: cf6547f110f7d83bf69ada9dafc64fd5ecd6fba6ccdb4de97c45caef0ff01316 4699240 clustalw-dbgsym_2.1+lgpl-6_i386.deb e3ddb8c29048cfef52e966ef9c1366501d7022d1a31b85221e81f0ba99fc4c43 4615 clustalw_2.1+lgpl-6_i386.buildinfo a14d9e3599773b83765eb87bb62debd989d229572f23369b9e47745560fd50ab 301408 clustalw_2.1+lgpl-6_i386.deb Files: 90277f45da796e28c0fbf4fddf733f7e 4699240 debug optional clustalw-dbgsym_2.1+lgpl-6_i386.deb 1f7c1705929e410b4e596b95cc7ab8b7 4615 science optional clustalw_2.1+lgpl-6_i386.buildinfo a7889ced0b1662d9025432323b3e83d9 301408 science optional clustalw_2.1+lgpl-6_i386.deb Tue Jul 28 02:27:34 UTC 2020 I: diffoscope 153 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.9nmKY62VF2/clustalw_2.1+lgpl-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.9nmKY62VF2/clustalw_2.1+lgpl-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.9nmKY62VF2/clustalw_2.1+lgpl-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.9nmKY62VF2/b1/clustalw_2.1+lgpl-6_i386.changes /srv/reproducible-results/rbuild-debian/tmp.9nmKY62VF2/b2/clustalw_2.1+lgpl-6_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.789s) 0.789s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.098s) 0.098s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 28 02:55:31 UTC 2020 I: diffoscope 153 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 28 02:55:31 UTC 2020 I: clustalw from buster built successfully and reproducibly on i386. Tue Jul 28 02:55:32 UTC 2020 I: Submitting .buildinfo files to external archives: Tue Jul 28 02:55:32 UTC 2020 I: Submitting 8.0K b1/clustalw_2.1+lgpl-6_i386.buildinfo.asc Tue Jul 28 02:55:33 UTC 2020 I: Submitting 8.0K b2/clustalw_2.1+lgpl-6_i386.buildinfo.asc Tue Jul 28 02:55:35 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 28 02:55:35 UTC 2020 I: Done submitting .buildinfo files. Tue Jul 28 02:55:35 UTC 2020 I: Removing signed clustalw_2.1+lgpl-6_i386.buildinfo.asc files: removed './b1/clustalw_2.1+lgpl-6_i386.buildinfo.asc' removed './b2/clustalw_2.1+lgpl-6_i386.buildinfo.asc'