https://launchpad.net/ubuntu/+source/clustalw/2.1+lgpl-6/+build/15122927 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-017 4.4.0-128-generic #154-Ubuntu SMP Fri May 25 14:15:18 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_163 python-lpbuildd_163 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.4 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 14 Jul 23:09:51 ntpdate[1891]: adjust time server 10.211.37.1 offset 0.004278 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15122927 /home/buildd/filecache-default/b7d07d6b68ae68badf26a018a3a0291d50e41e42 Creating target for build PACKAGEBUILD-15122927 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15122927 Starting target for build PACKAGEBUILD-15122927 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15122927 'deb http://ftpmaster.internal/ubuntu cosmic main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-security main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-updates main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15122927 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15122927 Updating target for build PACKAGEBUILD-15122927 Get:1 http://ftpmaster.internal/ubuntu cosmic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic-proposed InRelease [92.5 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 Packages [1021 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [516 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe amd64 Packages [8724 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [5023 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 Packages [76.6 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [36.4 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 Packages [214 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [113 kB] Fetched 16.2 MB in 4s (4024 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libargon2-0 libncursesw5 libprocps6 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libargon2-1 libncurses6 libncursesw6 libprocps7 libtinfo6 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils build-essential cpp cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv libapparmor1 libapt-pkg5.0 libargon2-0 libasan4 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libitm1 libkmod2 liblsan0 liblz4-1 libmount1 libmpx2 libncurses5 libncursesw5 libnpth0 libp11-kit0 libperl5.26 libpng16-16 libquadmath0 libreadline7 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libtsan0 libubsan0 libudev1 libusb-0.1-4 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common sed systemd systemd-sysv tar tzdata util-linux 105 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 56.9 MB of archives. After this operation, 2236 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main amd64 base-files amd64 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtinfo6 amd64 6.1+20180210-4ubuntu1 [84.0 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main amd64 debianutils amd64 4.8.6 [85.6 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main amd64 bash amd64 4.4.18-2ubuntu2 [614 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 bsdutils amd64 1:2.32-0.1ubuntu1 [60.4 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main amd64 tar amd64 1.30+dfsg-2 [240 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main amd64 dpkg amd64 1.19.0.5ubuntu3 [1140 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main amd64 libext2fs2 amd64 1.44.3-1 [158 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main amd64 e2fsprogs amd64 1.44.3-1 [396 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main amd64 ncurses-bin amd64 6.1+20180210-4ubuntu1 [163 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl-modules-5.26 all 5.26.2-6 [2762 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main amd64 libperl5.26 amd64 5.26.2-6 [3545 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl amd64 5.26.2-6 [202 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl-base amd64 5.26.2-6 [1391 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main amd64 sed amd64 4.5-1 [184 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main amd64 libuuid1 amd64 2.32-0.1ubuntu1 [19.9 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main amd64 libblkid1 amd64 2.32-0.1ubuntu1 [128 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfdisk1 amd64 2.32-0.1ubuntu1 [167 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncursesw6 amd64 6.1+20180210-4ubuntu1 [130 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libselinux1 amd64 2.8-1build1 [68.5 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmount1 amd64 2.32-0.1ubuntu1 [139 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsmartcols1 amd64 2.32-0.1ubuntu1 [86.0 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main amd64 fdisk amd64 2.32-0.1ubuntu1 [109 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main amd64 util-linux amd64 2.32-0.1ubuntu1 [916 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main amd64 base-passwd amd64 3.5.45 [47.4 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main amd64 ncurses-base all 6.1+20180210-4ubuntu1 [18.4 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libquadmath0 amd64 8.1.0-10ubuntu1 [133 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libitm1 amd64 8.1.0-10ubuntu1 [28.1 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gcc-8-base amd64 8.1.0-10ubuntu1 [19.0 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libgcc1 amd64 1:8.1.0-10ubuntu1 [40.7 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libmpx2 amd64 8.1.0-10ubuntu1 [11.7 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 liblsan0 amd64 8.1.0-10ubuntu1 [132 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libtsan0 amd64 8.1.0-10ubuntu1 [288 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libcc1-0 amd64 8.1.0-10ubuntu1 [39.6 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libatomic1 amd64 8.1.0-10ubuntu1 [9056 B] Get:36 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libgomp1 amd64 8.1.0-10ubuntu1 [76.4 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libstdc++6 amd64 8.1.0-10ubuntu1 [398 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblz4-1 amd64 1.8.2-1ubuntu1 [86.1 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libudev1 amd64 238-5ubuntu2 [56.1 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main amd64 libapt-pkg5.0 amd64 1.7.0~alpha2 [803 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 debconf all 1.5.67 [124 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main amd64 adduser all 3.117ubuntu1 [163 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libgpg-error0 amd64 1.32-1 [56.1 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgcrypt20 amd64 1.8.3-1ubuntu1 [419 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main amd64 gpgv amd64 2.2.8-1ubuntu1 [197 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main amd64 libseccomp2 amd64 2.3.3-3ubuntu1 [38.9 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main amd64 apt amd64 1.7.0~alpha2 [1172 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libapparmor1 amd64 2.12-4ubuntu6 [31.3 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main amd64 libaudit-common all 1:2.8.3-1ubuntu2 [4064 B] Get:50 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcap-ng0 amd64 0.7.9-1 [11.3 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main amd64 libaudit1 amd64 1:2.8.3-1ubuntu2 [38.6 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main amd64 libargon2-1 amd64 0~20171227-0.1 [20.2 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcryptsetup12 amd64 2:2.0.2-1ubuntu3 [134 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkmod2 amd64 25-1ubuntu1 [41.6 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main amd64 mount amd64 2.32-0.1ubuntu1 [104 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses6 amd64 6.1+20180210-4ubuntu1 [101 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main amd64 libprocps7 amd64 2:3.3.15-2ubuntu1 [32.6 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main amd64 procps amd64 2:3.3.15-2ubuntu1 [231 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 systemd amd64 238-5ubuntu2 [2930 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsystemd0 amd64 238-5ubuntu2 [208 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 systemd-sysv amd64 238-5ubuntu2 [13.7 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcom-err2 amd64 1.44.3-1 [9184 B] Get:63 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsepol1 amd64 2.8-1 [252 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsemanage-common all 2.8-1build1 [7000 B] Get:65 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsemanage1 amd64 2.8-1build1 [85.3 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main amd64 libss2 amd64 1.44.3-1 [11.1 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgmp10 amd64 2:6.1.2+dfsg-3 [240 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main amd64 libp11-kit0 amd64 0.23.12-2 [184 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtasn1-6 amd64 4.13-3 [36.1 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses5 amd64 6.1+20180210-4ubuntu1 [95.2 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncursesw5 amd64 6.1+20180210-4ubuntu1 [117 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtinfo5 amd64 6.1+20180210-4ubuntu1 [79.3 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main amd64 libargon2-0 amd64 0~20171227-0.1 [4532 B] Get:74 http://ftpmaster.internal/ubuntu cosmic/main amd64 readline-common all 7.0-5 [52.2 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main amd64 libreadline7 amd64 7.0-5 [123 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main amd64 libslang2 amd64 2.3.2-1ubuntu1 [425 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsqlite3-0 amd64 3.24.0-1 [506 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic/main amd64 libssl1.1 amd64 1.1.0g-2ubuntu5 [1129 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main amd64 openssl amd64 1.1.0g-2ubuntu5 [531 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main amd64 tzdata all 2018e-1 [188 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libpng16-16 amd64 1.6.34-2 [176 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils-x86-64-linux-gnu amd64 2.30-22ubuntu1 [1855 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils-common amd64 2.30-22ubuntu1 [193 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils amd64 2.30-22ubuntu1 [3392 B] Get:85 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbinutils amd64 2.30-22ubuntu1 [502 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libasan4 amd64 7.3.0-25ubuntu1 [358 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libubsan0 amd64 7.3.0-25ubuntu1 [126 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libcilkrts5 amd64 7.3.0-25ubuntu1 [42.5 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 g++-7 amd64 7.3.0-25ubuntu1 [7573 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gcc-7 amd64 7.3.0-25ubuntu1 [7455 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libstdc++-7-dev amd64 7.3.0-25ubuntu1 [1464 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libgcc-7-dev amd64 7.3.0-25ubuntu1 [2377 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 cpp-7 amd64 7.3.0-25ubuntu1 [6737 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gcc-7-base amd64 7.3.0-25ubuntu1 [19.0 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main amd64 cpp amd64 4:7.3.0-3ubuntu3 [27.5 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc amd64 4:7.3.0-3ubuntu3 [5216 B] Get:97 http://ftpmaster.internal/ubuntu cosmic/main amd64 g++ amd64 4:7.3.0-3ubuntu3 [1592 B] Get:98 http://ftpmaster.internal/ubuntu cosmic/main amd64 dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic/main amd64 libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic/main amd64 build-essential amd64 12.5ubuntu2 [4732 B] Get:101 http://ftpmaster.internal/ubuntu cosmic/main amd64 e2fslibs amd64 1.44.3-1 [2704 B] Get:102 http://ftpmaster.internal/ubuntu cosmic/main amd64 pinentry-curses amd64 1.1.0-1build2 [35.9 kB] Get:103 http://ftpmaster.internal/ubuntu cosmic/main amd64 libnpth0 amd64 1.5-4 [7708 B] Get:104 http://ftpmaster.internal/ubuntu cosmic/main amd64 gpg amd64 2.2.8-1ubuntu1 [470 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main amd64 gpgconf amd64 2.2.8-1ubuntu1 [122 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/main amd64 gpg-agent amd64 2.2.8-1ubuntu1 [228 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcomerr2 amd64 1.44.3-1 [2704 B] Get:108 http://ftpmaster.internal/ubuntu cosmic/main amd64 libusb-0.1-4 amd64 2:0.1.12-32 [17.4 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 linux-libc-dev amd64 4.17.0-5.6 [1003 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic/main amd64 pkgbinarymangler all 139 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.9 MB in 2s (32.1 MB/s) (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_amd64.deb ... Unpacking base-files (10.1ubuntu4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu4) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Selecting previously unselected package libtinfo6:amd64. (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-4ubuntu1_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20180210-4ubuntu1) ... Setting up libtinfo6:amd64 (6.1+20180210-4ubuntu1) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_amd64.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_amd64.deb ... Unpacking bash (4.4.18-2ubuntu2) over (4.4.18-2ubuntu1) ... Setting up bash (4.4.18-2ubuntu2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.32-0.1ubuntu1_amd64.deb ... Unpacking bsdutils (1:2.32-0.1ubuntu1) over (1:2.31.1-0.4ubuntu3) ... Setting up bsdutils (1:2.32-0.1ubuntu1) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-2_amd64.deb ... Unpacking tar (1.30+dfsg-2) over (1.29b-2) ... Setting up tar (1.30+dfsg-2) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.5ubuntu3_amd64.deb ... Unpacking dpkg (1.19.0.5ubuntu3) over (1.19.0.5ubuntu2) ... Setting up dpkg (1.19.0.5ubuntu3) ... (Reading database ... 12646 files and directories currently installed.) 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Setting up libmpx2:amd64 (8.1.0-10ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up libperl5.26:amd64 (5.26.2-6) ... Setting up libssl1.1:amd64 (1.1.0g-2ubuntu5) ... Setting up openssl (1.1.0g-2ubuntu5) ... Setting up libsqlite3-0:amd64 (3.24.0-1) ... Setting up pinentry-curses (1.1.0-1build2) ... Setting up libcomerr2:amd64 (1.44.3-1) ... Setting up libslang2:amd64 (2.3.2-1ubuntu1) ... Setting up libusb-0.1-4:amd64 (2:0.1.12-32) ... Setting up libitm1:amd64 (8.1.0-10ubuntu1) ... Setting up gpg (2.2.8-1ubuntu1) ... Setting up libasan4:amd64 (7.3.0-25ubuntu1) ... Setting up libbinutils:amd64 (2.30-22ubuntu1) ... Setting up libcilkrts5:amd64 (7.3.0-25ubuntu1) ... Setting up libubsan0:amd64 (7.3.0-25ubuntu1) ... Setting up gpg-agent (2.2.8-1ubuntu1) ... Setting up libgcc-7-dev:amd64 (7.3.0-25ubuntu1) ... Setting up cpp-7 (7.3.0-25ubuntu1) ... Setting up libstdc++-7-dev:amd64 (7.3.0-25ubuntu1) ... Setting up perl (5.26.2-6) ... Setting up binutils-x86-64-linux-gnu (2.30-22ubuntu1) ... Setting up cpp (4:7.3.0-3ubuntu3) ... Setting up libdpkg-perl (1.19.0.5ubuntu3) ... Setting up binutils (2.30-22ubuntu1) ... Setting up gcc-7 (7.3.0-25ubuntu1) ... Setting up g++-7 (7.3.0-25ubuntu1) ... Setting up gcc (4:7.3.0-3ubuntu3) ... Setting up dpkg-dev (1.19.0.5ubuntu3) ... Setting up g++ (4:7.3.0-3ubuntu3) ... Setting up build-essential (12.5ubuntu2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15122927 amd64 cosmic-proposed -c chroot:build-PACKAGEBUILD-15122927 --arch=amd64 --dist=cosmic-proposed --nolog -A clustalw_2.1+lgpl-6.dsc Initiating build PACKAGEBUILD-15122927 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-128-generic #154-Ubuntu SMP Fri May 25 14:15:18 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-017.buildd +==============================================================================+ | clustalw 2.1+lgpl-6 (amd64) 14 Jul 2018 23:10 | +==============================================================================+ Package: clustalw Version: 2.1+lgpl-6 Source Version: 2.1+lgpl-6 Distribution: cosmic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/clustalw-v4qyKr/clustalw-2.1+lgpl' with '<>' I: NOTICE: Log filtering will replace 'build/clustalw-v4qyKr' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15122927/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- clustalw_2.1+lgpl-6.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-nVikx2/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-nVikx2/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nVikx2/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-nVikx2/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nVikx2/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-nVikx2/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libargon2-0 libncursesw5 libprocps6 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-nVikx2/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12696 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~) Filtered Build-Depends: debhelper (>= 11~) dpkg-deb: building package 'sbuild-build-depends-clustalw-dummy' in '/<>/resolver-02fOWZ/apt_archive/sbuild-build-depends-clustalw-dummy.deb'. Ign:1 copy:/<>/resolver-02fOWZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-02fOWZ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-02fOWZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-02fOWZ/apt_archive ./ Sources [211 B] Get:5 copy:/<>/resolver-02fOWZ/apt_archive ./ Packages [529 B] Fetched 2859 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install clustalw build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libargon2-0 libncursesw5 libprocps6 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-clustalw-dummy 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 16.7 MB of archives. After this operation, 63.0 MB of additional disk space will be used. Get:1 copy:/<>/resolver-02fOWZ/apt_archive ./ sbuild-build-depends-clustalw-dummy 0.invalid.0 [860 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbsd0 amd64 0.9.1-1 [44.6 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main amd64 groff-base amd64 1.22.3-10 [1153 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpipeline1 amd64 1.5.0-1 [25.3 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main amd64 man-db amd64 2.8.3-2 [1019 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmagic-mgc amd64 1:5.33-3 [192 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmagic1 amd64 1:5.33-3 [69.8 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main amd64 file amd64 1:5.33-3 [22.9 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main amd64 libelf1 amd64 0.170-0.5 [44.1 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main amd64 libglib2.0-0 amd64 2.56.1-2ubuntu1 [1167 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main amd64 libicu60 amd64 60.2-6ubuntu1 [8055 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libxml2 amd64 2.9.4+dfsg1-7build1 [664 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main amd64 gettext-base amd64 0.19.8.1-6build1 [50.0 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main amd64 autoconf all 2.69-11 [322 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main amd64 automake all 1:1.15.1-3ubuntu2 [509 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main amd64 autopoint all 0.19.8.1-6build1 [412 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtool all 2.4.6-2.1 [195 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main amd64 dh-autoreconf all 19 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main amd64 libarchive-zip-perl all 1.60-1ubuntu1 [84.6 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfile-stripnondeterminism-perl all 0.042-1 [15.2 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main amd64 dh-strip-nondeterminism all 0.042-1 [5188 B] Get:27 http://ftpmaster.internal/ubuntu cosmic/main amd64 dwz amd64 0.12-2 [77.7 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcroco3 amd64 0.6.12-2 [81.3 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main amd64 gettext amd64 0.19.8.1-6build1 [895 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main amd64 po-debconf all 1.0.20 [232 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main amd64 debhelper all 11.3.2ubuntu1 [883 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.7 MB in 0s (106 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12696 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_amd64.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_amd64.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.3-2_amd64.deb ... Unpacking man-db (2.8.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.33-3_amd64.deb ... Unpacking libmagic-mgc (1:5.33-3) ... Selecting previously unselected package libmagic1:amd64. 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Unpacking debhelper (11.3.2ubuntu1) ... Selecting previously unselected package sbuild-build-depends-clustalw-dummy. Preparing to unpack .../31-sbuild-build-depends-clustalw-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-clustalw-dummy (0.invalid.0) ... Setting up libicu60:amd64 (60.2-6ubuntu1) ... Setting up libarchive-zip-perl (1.60-1ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libelf1:amd64 (0.170-0.5) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:amd64 (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-6build1) ... Setting up libpipeline1:amd64 (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7build1) ... Setting up libmagic-mgc (1:5.33-3) ... Setting up libmagic1:amd64 (1:5.33-3) ... Setting up libcroco3:amd64 (0.6.12-2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-6build1) ... Setting up libfile-stripnondeterminism-perl (0.042-1) ... Setting up gettext (0.19.8.1-6build1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.33-3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2.1) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (0.042-1) ... Setting up debhelper (11.3.2ubuntu1) ... Setting up sbuild-build-depends-clustalw-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-128-generic amd64 (x86_64) Toolchain package versions: binutils_2.30-22ubuntu1 dpkg-dev_1.19.0.5ubuntu3 g++-7_7.3.0-25ubuntu1 gcc-7_7.3.0-25ubuntu1 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-25ubuntu1 libstdc++6_8.1.0-10ubuntu1 linux-libc-dev_4.17.0-5.6 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0~alpha2 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6build1 autotools-dev_20180224.1 base-files_10.1ubuntu4 base-passwd_3.5.45 bash_4.4.18-2ubuntu2 binutils_2.30-22ubuntu1 binutils-common_2.30-22ubuntu1 binutils-x86-64-linux-gnu_2.30-22ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu3 cpp-7_7.3.0-25ubuntu1 dash_0.5.8-2.10 debconf_1.5.67 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu3 dpkg-dev_1.19.0.5ubuntu3 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu1 file_1:5.33-3 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu3 g++-7_7.3.0-25ubuntu1 gcc_4:7.3.0-3ubuntu3 gcc-7_7.3.0-25ubuntu1 gcc-7-base_7.3.0-25ubuntu1 gcc-8-base_8.1.0-10ubuntu1 gettext_0.19.8.1-6build1 gettext-base_0.19.8.1-6build1 gpg_2.2.8-1ubuntu1 gpg-agent_2.2.8-1ubuntu1 gpgconf_2.2.8-1ubuntu1 gpgv_2.2.8-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu6 libapt-pkg5.0_1.7.0~alpha2 libarchive-zip-perl_1.60-1ubuntu1 libargon2-0_0~20171227-0.1 libargon2-1_0~20171227-0.1 libasan4_7.3.0-25ubuntu1 libassuan0_2.5.1-2 libatomic1_8.1.0-10ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu2 libaudit1_1:2.8.3-1ubuntu2 libbinutils_2.30-22ubuntu1 libblkid1_2.32-0.1ubuntu1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-10ubuntu1 libcilkrts5_7.3.0-25ubuntu1 libcom-err2_1.44.3-1 libcomerr2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu3 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu3 libelf1_0.170-0.5 libext2fs2_1.44.3-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libgcc-7-dev_7.3.0-25ubuntu1 libgcc1_1:8.1.0-10ubuntu1 libgcrypt20_1.8.3-1ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.1.0-10ubuntu1 libgpg-error0_1.32-1 libhogweed4_3.4-1 libicu60_60.2-6ubuntu1 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libitm1_8.1.0-10ubuntu1 libjson-c3_0.12.1-1.3 libkmod2_25-1ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.1.0-10ubuntu1 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1ubuntu1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libmpx2_8.1.0-10ubuntu1 libncurses5_6.1+20180210-4ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw5_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnpth0_1.5-4 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-9 libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libpng16-16_1.6.34-2 libprocps6_2:3.3.12-3ubuntu1 libprocps7_2:3.3.15-2ubuntu1 libquadmath0_8.1.0-10ubuntu1 libreadline7_7.0-5 libseccomp2_2.3.3-3ubuntu1 libselinux1_2.8-1build1 libsemanage-common_2.8-1build1 libsemanage1_2.8-1build1 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl1.1_1.1.0g-2ubuntu5 libstdc++-7-dev_7.3.0-25ubuntu1 libstdc++6_8.1.0-10ubuntu1 libsystemd0_238-5ubuntu2 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4ubuntu1 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-2.1 libtsan0_8.1.0-10ubuntu1 libubsan0_7.3.0-25ubuntu1 libudev1_238-5ubuntu2 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu1 libxml2_2.9.4+dfsg1-7build1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.17.0-5.6 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mount_2.32-0.1ubuntu1 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.0g-2ubuntu5 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1build2 pkgbinarymangler_139 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 readline-common_7.0-5 sbuild-build-depends-clustalw-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_238-5ubuntu2 systemd-sysv_238-5ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.30+dfsg-2 tzdata_2018e-1 ubuntu-keyring_2018.02.28 util-linux_2.32-0.1ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jul 14 15:12:38 2018 UTC 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: applying spelling.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15122927 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15122927 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15122927 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package clustalw dpkg-buildpackage: info: source version 2.1+lgpl-6 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build clustalw-2.1+lgpl dpkg-buildpackage: info: host architecture amd64 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=x86_64-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/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-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 for style of include used by make... GNU 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 -j4 make[1]: Entering directory '/<>/clustalw-2.1+lgpl' Making all in m4 make[2]: Entering directory '/<>/clustalw-2.1+lgpl/m4' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/clustalw-2.1+lgpl/m4' Making all in src make[2]: Entering directory '/<>/clustalw-2.1+lgpl/src' make all-recursive make[3]: Entering directory '/<>/clustalw-2.1+lgpl/src' make[4]: Entering directory '/<>/clustalw-2.1+lgpl/src' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:8:0, 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:8:0, 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:29:0: ./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++/7/memory:80:0, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:23:0, 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++/7/memory:80:0, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.h:8:0, 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++/7/memory:80:0, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:9:0: ./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++/7/memory:80:0, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11:0: ./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++/7/memory:80:0, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11:0: ./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++/7/memory:80:0, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:4:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedGuideTree.cpp:10: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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:8:0, 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:8:0, 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/Tree.cpp:10:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:23:0, 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++/7/memory:80:0, from ./tree/ClusterTree.h:16, from ./tree/ClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/ClusterTree.cpp:9:0: ./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++/7/memory:80:0, from ./tree/ClusterTree.h:16, from ./tree/ClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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"); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp In file included from ./tree/TreeInterface.cpp:15:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/ClusterTree.h:23:0, 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UnRootedClusterTree.h:8:0, 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:18:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:23:0: ./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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:23:0, 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++/7/memory:80:0, from ./tree/ClusterTree.h:16, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UnRootedClusterTree.h:8:0, 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++/7/memory:80:0, from ./tree/ClusterTree.h:16, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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:8:0, 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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:18:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./substitutionMatrix/SubMatrix.cpp:15:0: ./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:8:0, 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:18:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/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++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ ./interface/InteractiveMenu.cpp: In member function ‘void clustalw::InteractiveMenu::doSystem()’: ./interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(lin1.c_str()); ~~~~~~^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:17:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ ./multipleAlign/Iteration.cpp: In member function ‘bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)’: ./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] tmpnam (buffer); ~~~~~~~^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/MSA.h:10, from ./multipleAlign/MSA.cpp:16: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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"); ^~~~~~~~~~~~~~ In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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"); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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"); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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"); ^~~~~~~~~~~~~~ In file included from ./general/OutputFile.cpp:9:0: ./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++/7/memory:80:0, from ./general/OutputFile.h:8, from ./general/OutputFile.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp In file included from ./general/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:8:0, 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"); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8:0, 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:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27:0: ./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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/memory:80:0, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8:0, 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"); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/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 -fdebug-prefix-map=/<>/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 ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./Clustal.h:18, from ./Clustal.cpp:27: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./Clustal.h:18:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./alignment/Alignment.h:42, from ./main.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./main.cpp:16:0: ./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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20:0, 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++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 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 '/<>/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/<>/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/<>/clustalw-2.1+lgpl/src' make[2]: Entering directory '/<>/clustalw-2.1+lgpl' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/<>/clustalw-2.1+lgpl' make[1]: Leaving directory '/<>/clustalw-2.1+lgpl' dh_auto_test make -j4 check VERBOSE=1 make[1]: Entering directory '/<>/clustalw-2.1+lgpl' Making check in m4 make[2]: Entering directory '/<>/clustalw-2.1+lgpl/m4' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/clustalw-2.1+lgpl/m4' Making check in src make[2]: Entering directory '/<>/clustalw-2.1+lgpl/src' make[3]: Entering directory '/<>/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/<>/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/<>/clustalw-2.1+lgpl/src' make[2]: Entering directory '/<>/clustalw-2.1+lgpl' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/<>/clustalw-2.1+lgpl' make[1]: Leaving directory '/<>/clustalw-2.1+lgpl' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j4 install DESTDIR=/<>/clustalw-2.1\+lgpl/debian/clustalw AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>/clustalw-2.1+lgpl' Making install in m4 make[2]: Entering directory '/<>/clustalw-2.1+lgpl/m4' make[3]: Entering directory '/<>/clustalw-2.1+lgpl/m4' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Leaving directory '/<>/clustalw-2.1+lgpl/m4' make[2]: Leaving directory '/<>/clustalw-2.1+lgpl/m4' Making install in src make[2]: Entering directory '/<>/clustalw-2.1+lgpl/src' make[3]: Entering directory '/<>/clustalw-2.1+lgpl/src' make[4]: Entering directory '/<>/clustalw-2.1+lgpl/src' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/clustalw-2.1+lgpl/debian/clustalw/usr/bin' /usr/bin/install -c clustalw2 '/<>/clustalw-2.1+lgpl/debian/clustalw/usr/bin' make[4]: Leaving directory '/<>/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/<>/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/<>/clustalw-2.1+lgpl/src' make[2]: Entering directory '/<>/clustalw-2.1+lgpl' make[3]: Entering directory '/<>/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 '/<>/clustalw-2.1+lgpl' make[2]: Leaving directory '/<>/clustalw-2.1+lgpl' make[1]: Leaving directory '/<>/clustalw-2.1+lgpl' debian/rules override_dh_install make[1]: Entering directory '/<>/clustalw-2.1+lgpl' dh_install # We have to ask upstream if it is important for them that the binary is named clustalw2 mv /<>/clustalw-2.1+lgpl/debian/clustalw/usr/bin/clustalw2 /<>/clustalw-2.1+lgpl/debian/clustalw/usr/bin/clustalw make[1]: Leaving directory '/<>/clustalw-2.1+lgpl' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/clustalw-2.1+lgpl' dh_installchangelogs debian/CHANGELOG.upstream make[1]: Leaving directory '/<>/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 INFO: pkgstriptranslations version 139 INFO: pkgstriptranslations version 139 pkgstriptranslations: processing clustalw (in debian/clustalw); do_strip: , oemstrip: pkgstriptranslations: processing clustalw-dbgsym (in debian/.debhelper/clustalw/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/clustalw/DEBIAN/control, package clustalw, directory debian/clustalw .. removing usr/share/doc/clustalw/changelog.gz pkgstripfiles: processing control file: debian/.debhelper/clustalw/dbgsym-root/DEBIAN/control, package clustalw-dbgsym, directory debian/.debhelper/clustalw/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package clustalw-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'clustalw-dbgsym' in 'debian/.debhelper/scratch-space/build-clustalw/clustalw-dbgsym_2.1+lgpl-6_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/clustalw/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package clustalw ... pkgstripfiles: No PNG files. dpkg-deb: building package 'clustalw' in '../clustalw_2.1+lgpl-6_amd64.deb'. Renaming clustalw-dbgsym_2.1+lgpl-6_amd64.deb to clustalw-dbgsym_2.1+lgpl-6_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../clustalw_2.1+lgpl-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build clustalw-2.1+lgpl dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180714-2311 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ clustalw_2.1+lgpl-6_amd64.changes: ---------------------------------- Format: 1.8 Date: Sat, 14 Jul 2018 17:09:36 +0200 Source: clustalw Binary: clustalw Architecture: amd64 Version: 2.1+lgpl-6 Distribution: cosmic-proposed Urgency: medium Maintainer: Launchpad Build Daemon 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: 8814957de4bc9c6fcbeb2de0c392ac5217679a59 3271516 clustalw-dbgsym_2.1+lgpl-6_amd64.ddeb 16070807ec3f5a3cf9729afbb650b46591553cf2 5018 clustalw_2.1+lgpl-6_amd64.buildinfo 64b138b976a36995a6b9517caa1509f52b653584 275836 clustalw_2.1+lgpl-6_amd64.deb Checksums-Sha256: 1bc8714944adb002b9426f7d63b3911014edeb65390e22c45159e8fc07aba99c 3271516 clustalw-dbgsym_2.1+lgpl-6_amd64.ddeb df7c5ee4524880163f5b8b5cb8be833d764334f633393441b32405c75a2ca5c0 5018 clustalw_2.1+lgpl-6_amd64.buildinfo 6548be721710fb1306a2900b47155539dbc1468edc0e1af73de776354102414b 275836 clustalw_2.1+lgpl-6_amd64.deb Files: b1b25408bddb61067f916e1c494c9472 3271516 debug optional clustalw-dbgsym_2.1+lgpl-6_amd64.ddeb e42ba820f54f9c36f0f9015d4813d11e 5018 science optional clustalw_2.1+lgpl-6_amd64.buildinfo 2919644ed143bedb1a6000c790394c82 275836 science optional clustalw_2.1+lgpl-6_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ clustalw_2.1+lgpl-6_amd64.deb ----------------------------- new debian package, version 2.0. size 275836 bytes: control archive=1500 bytes. 1173 bytes, 23 lines control 878 bytes, 12 lines md5sums 199 bytes, 7 lines * postinst #!/bin/sh 174 bytes, 5 lines * postrm #!/bin/sh Package: clustalw Version: 2.1+lgpl-6 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 771 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2) Suggests: clustalx, seaview Enhances: bioperl-run, emboss, t-coffee Section: science Priority: optional Homepage: http://www.clustal.org/clustal2/ Description: global multiple nucleotide or peptide sequence alignment This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. Clustal W is very well accepted. . The output of Clustal W can be edited manually but preferably with an alignment editor like SeaView or within its companion Clustal X. When building a model from your alignment, this can be applied for improved database searches. The Debian package hmmer creates such in form of an HMM. drwxr-xr-x root/root 0 2018-07-14 15:09 ./ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/bin/ -rwxr-xr-x root/root 713952 2018-07-14 15:09 ./usr/bin/clustalw drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/clustalw/ -rw-r--r-- root/root 33751 2018-07-14 15:09 ./usr/share/clustalw/clustalw_help drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/clustalw/ -rw-r--r-- root/root 715 2010-09-09 14:26 ./usr/share/doc/clustalw/README -rw-r--r-- root/root 821 2018-07-14 15:09 ./usr/share/doc/clustalw/README.Debian -rw-r--r-- root/root 1920 2018-07-14 15:09 ./usr/share/doc/clustalw/changelog.Debian.gz -rw-r--r-- root/root 2091 2018-07-14 15:09 ./usr/share/doc/clustalw/copyright drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/ -rw-r--r-- root/root 552 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/Makefile -rw-r--r-- root/root 1007 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/nuc.data -rw-r--r-- root/root 1013 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/nuc2.data -rw-r--r-- root/root 157 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/seq drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/man/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/man/man1/ -rw-r--r-- root/root 4184 2018-07-14 15:09 ./usr/share/man/man1/clustalw.1.gz drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/menu/ -rw-r--r-- root/root 193 2018-07-14 15:09 ./usr/share/menu/clustalw +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 52236 Build-Time: 44 Distribution: cosmic-proposed Host Architecture: amd64 Install-Time: 11 Job: clustalw_2.1+lgpl-6.dsc Machine Architecture: amd64 Package: clustalw Package-Time: 55 Source-Version: 2.1+lgpl-6 Space: 52236 Status: successful Version: 2.1+lgpl-6 -------------------------------------------------------------------------------- Finished at 20180714-2311 Build needed 00:00:55, 52236k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15122927 Scanning for processes to kill in build PACKAGEBUILD-15122927