https://launchpad.net/ubuntu/+source/clustalw/2.1+lgpl-6/+build/15122929 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-038 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:52:48 UTC 2018 aarch64 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 23:09:32 ntpdate[1863]: adjust time server 10.211.37.1 offset -0.001296 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15122929 /home/buildd/filecache-default/fc6c56f66744d62233b3c844f67cb7d83d839bbc Creating target for build PACKAGEBUILD-15122929 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15122929 Starting target for build PACKAGEBUILD-15122929 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15122929 '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-15122929 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15122929 Updating target for build PACKAGEBUILD-15122929 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 armhf Packages [972 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [516 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe armhf Packages [8414 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [5023 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf Packages [57.4 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [36.4 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe armhf Packages [198 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [113 kB] Fetched 15.8 MB in 6s (2599 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-arm-linux-gnueabihf binutils-common 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 libkmod2 liblz4-1 libmount1 libncurses5 libncursesw5 libnpth0 libp11-kit0 libperl5.26 libpng16-16 libreadline7 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 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 100 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 47.9 MB of archives. After this operation, 1746 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main armhf base-files armhf 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main armhf libtinfo6 armhf 6.1+20180210-4ubuntu1 [71.2 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main armhf debianutils armhf 4.8.6 [84.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main armhf bash armhf 4.4.18-2ubuntu2 [552 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main armhf bsdutils armhf 1:2.32-0.1ubuntu1 [55.5 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main armhf tar armhf 1.30+dfsg-2 [218 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main armhf dpkg armhf 1.19.0.5ubuntu3 [1096 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main armhf libext2fs2 armhf 1.44.3-1 [145 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main armhf e2fsprogs armhf 1.44.3-1 [375 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main armhf ncurses-bin armhf 6.1+20180210-4ubuntu1 [155 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main armhf perl-modules-5.26 all 5.26.2-6 [2762 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main armhf libperl5.26 armhf 5.26.2-6 [2870 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main armhf perl armhf 5.26.2-6 [202 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main armhf perl-base armhf 5.26.2-6 [1291 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main armhf sed armhf 4.5-1 [177 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main armhf libuuid1 armhf 2.32-0.1ubuntu1 [19.2 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main armhf libblkid1 armhf 2.32-0.1ubuntu1 [115 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main armhf libfdisk1 armhf 2.32-0.1ubuntu1 [155 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main armhf libncursesw6 armhf 6.1+20180210-4ubuntu1 [104 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libselinux1 armhf 2.8-1build1 [59.2 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main armhf libmount1 armhf 2.32-0.1ubuntu1 [125 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main armhf libsmartcols1 armhf 2.32-0.1ubuntu1 [76.2 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main armhf fdisk armhf 2.32-0.1ubuntu1 [98.7 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main armhf util-linux armhf 2.32-0.1ubuntu1 [858 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main armhf base-passwd armhf 3.5.45 [46.0 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main armhf ncurses-base all 6.1+20180210-4ubuntu1 [18.4 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgomp1 armhf 8.1.0-10ubuntu1 [66.6 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gcc-8-base armhf 8.1.0-10ubuntu1 [19.1 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgcc1 armhf 1:8.1.0-10ubuntu1 [37.1 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libcc1-0 armhf 8.1.0-10ubuntu1 [32.7 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libatomic1 armhf 8.1.0-10ubuntu1 [7048 B] Get:32 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libstdc++6 armhf 8.1.0-10ubuntu1 [350 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main armhf liblz4-1 armhf 1.8.2-1ubuntu1 [76.1 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libudev1 armhf 238-5ubuntu2 [50.7 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main armhf libapt-pkg5.0 armhf 1.7.0~alpha2 [731 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf debconf all 1.5.67 [124 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main armhf adduser all 3.117ubuntu1 [163 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgpg-error0 armhf 1.32-1 [48.4 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main armhf libgcrypt20 armhf 1.8.3-1ubuntu1 [364 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main armhf gpgv armhf 2.2.8-1ubuntu1 [167 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main armhf libseccomp2 armhf 2.3.3-3ubuntu1 [30.4 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main armhf apt armhf 1.7.0~alpha2 [1127 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libapparmor1 armhf 2.12-4ubuntu6 [27.1 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main armhf libaudit-common all 1:2.8.3-1ubuntu2 [4064 B] Get:45 http://ftpmaster.internal/ubuntu cosmic/main armhf libcap-ng0 armhf 0.7.9-1 [10.1 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main armhf libaudit1 armhf 1:2.8.3-1ubuntu2 [35.5 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main armhf libargon2-1 armhf 0~20171227-0.1 [20.7 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main armhf libcryptsetup12 armhf 2:2.0.2-1ubuntu3 [119 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main armhf libkmod2 armhf 25-1ubuntu1 [35.7 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main armhf mount armhf 2.32-0.1ubuntu1 [97.4 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses6 armhf 6.1+20180210-4ubuntu1 [78.5 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main armhf libprocps7 armhf 2:3.3.15-2ubuntu1 [29.6 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main armhf procps armhf 2:3.3.15-2ubuntu1 [219 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf systemd armhf 238-5ubuntu2 [2783 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libsystemd0 armhf 238-5ubuntu2 [189 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf systemd-sysv armhf 238-5ubuntu2 [13.7 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main armhf libcom-err2 armhf 1.44.3-1 [8356 B] Get:58 http://ftpmaster.internal/ubuntu cosmic/main armhf libsepol1 armhf 2.8-1 [219 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main armhf libsemanage-common all 2.8-1build1 [7000 B] Get:60 http://ftpmaster.internal/ubuntu cosmic/main armhf libsemanage1 armhf 2.8-1build1 [73.0 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main armhf libss2 armhf 1.44.3-1 [9396 B] Get:62 http://ftpmaster.internal/ubuntu cosmic/main armhf libgmp10 armhf 2:6.1.2+dfsg-3 [182 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main armhf libp11-kit0 armhf 0.23.12-2 [163 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main armhf libtasn1-6 armhf 4.13-3 [31.1 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses5 armhf 6.1+20180210-4ubuntu1 [74.9 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main armhf libncursesw5 armhf 6.1+20180210-4ubuntu1 [95.3 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main armhf libtinfo5 armhf 6.1+20180210-4ubuntu1 [67.6 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main armhf libargon2-0 armhf 0~20171227-0.1 [4536 B] Get:69 http://ftpmaster.internal/ubuntu cosmic/main armhf readline-common all 7.0-5 [52.2 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/main armhf libreadline7 armhf 7.0-5 [102 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main armhf libslang2 armhf 2.3.2-1ubuntu1 [383 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libsqlite3-0 armhf 3.24.0-1 [429 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main armhf libssl1.1 armhf 1.1.0g-2ubuntu5 [912 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main armhf openssl armhf 1.1.0g-2ubuntu5 [510 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main armhf tzdata all 2018e-1 [188 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libpng16-16 armhf 1.6.34-2 [159 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main armhf libbinutils armhf 2.30-22ubuntu1 [309 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils-common armhf 2.30-22ubuntu1 [193 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils armhf 2.30-22ubuntu1 [3352 B] Get:80 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils-arm-linux-gnueabihf armhf 2.30-22ubuntu1 [2175 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libasan4 armhf 7.3.0-25ubuntu1 [327 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libubsan0 armhf 7.3.0-25ubuntu1 [108 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libcilkrts5 armhf 7.3.0-25ubuntu1 [35.9 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf g++-7 armhf 7.3.0-25ubuntu1 [6048 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gcc-7 armhf 7.3.0-25ubuntu1 [5953 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libstdc++-7-dev armhf 7.3.0-25ubuntu1 [1536 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgcc-7-dev armhf 7.3.0-25ubuntu1 [706 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf cpp-7 armhf 7.3.0-25ubuntu1 [5298 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gcc-7-base armhf 7.3.0-25ubuntu1 [19.1 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic/main armhf cpp armhf 4:7.3.0-3ubuntu3 [27.6 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc armhf 4:7.3.0-3ubuntu3 [5228 B] Get:92 http://ftpmaster.internal/ubuntu cosmic/main armhf g++ armhf 4:7.3.0-3ubuntu3 [1600 B] Get:93 http://ftpmaster.internal/ubuntu cosmic/main armhf dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic/main armhf libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main armhf build-essential armhf 12.5ubuntu2 [4732 B] Get:96 http://ftpmaster.internal/ubuntu cosmic/main armhf e2fslibs armhf 1.44.3-1 [2704 B] Get:97 http://ftpmaster.internal/ubuntu cosmic/main armhf pinentry-curses armhf 1.1.0-1build2 [31.4 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic/main armhf libnpth0 armhf 1.5-4 [6648 B] Get:99 http://ftpmaster.internal/ubuntu cosmic/main armhf gpg armhf 2.2.8-1ubuntu1 [411 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic/main armhf gpgconf armhf 2.2.8-1ubuntu1 [105 kB] Get:101 http://ftpmaster.internal/ubuntu cosmic/main armhf gpg-agent armhf 2.2.8-1ubuntu1 [189 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/main armhf libcomerr2 armhf 1.44.3-1 [2704 B] Get:103 http://ftpmaster.internal/ubuntu cosmic/main armhf libusb-0.1-4 armhf 2:0.1.12-32 [15.6 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf linux-libc-dev armhf 4.17.0-5.6 [985 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main armhf pkgbinarymangler all 139 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.9 MB in 8s (5783 kB/s) (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_armhf.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:armhf. (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-4ubuntu1_armhf.deb ... Unpacking libtinfo6:armhf (6.1+20180210-4ubuntu1) ... Setting up libtinfo6:armhf (6.1+20180210-4ubuntu1) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_armhf.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_armhf.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 ... 12387 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.32-0.1ubuntu1_armhf.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 ... 12387 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-2_armhf.deb ... Unpacking tar (1.30+dfsg-2) over (1.29b-2) ... Setting up tar (1.30+dfsg-2) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.5ubuntu3_armhf.deb ... Unpacking dpkg (1.19.0.5ubuntu3) over (1.19.0.5ubuntu2) ... Setting up dpkg (1.19.0.5ubuntu3) ... (Reading database ... 12387 files and directories currently installed.) 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Setting up linux-libc-dev:armhf (4.17.0-5.6) ... Setting up perl-modules-5.26 (5.26.2-6) ... Setting up libargon2-0 (0~20171227-0.1) ... Setting up gcc-7-base:armhf (7.3.0-25ubuntu1) ... Setting up binutils-common:armhf (2.30-22ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up libperl5.26:armhf (5.26.2-6) ... Setting up libssl1.1:armhf (1.1.0g-2ubuntu5) ... Setting up openssl (1.1.0g-2ubuntu5) ... Setting up libsqlite3-0:armhf (3.24.0-1) ... Setting up pinentry-curses (1.1.0-1build2) ... Setting up libcomerr2:armhf (1.44.3-1) ... Setting up libslang2:armhf (2.3.2-1ubuntu1) ... Setting up libusb-0.1-4:armhf (2:0.1.12-32) ... Setting up gpg (2.2.8-1ubuntu1) ... Setting up libasan4:armhf (7.3.0-25ubuntu1) ... Setting up libbinutils:armhf (2.30-22ubuntu1) ... Setting up libcilkrts5:armhf (7.3.0-25ubuntu1) ... Setting up libubsan0:armhf (7.3.0-25ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.30-22ubuntu1) ... Setting up gpg-agent (2.2.8-1ubuntu1) ... Setting up libgcc-7-dev:armhf (7.3.0-25ubuntu1) ... Setting up cpp-7 (7.3.0-25ubuntu1) ... Setting up libstdc++-7-dev:armhf (7.3.0-25ubuntu1) ... Setting up perl (5.26.2-6) ... Setting up binutils (2.30-22ubuntu1) ... Setting up cpp (4:7.3.0-3ubuntu3) ... Setting up gcc-7 (7.3.0-25ubuntu1) ... Setting up g++-7 (7.3.0-25ubuntu1) ... Setting up libdpkg-perl (1.19.0.5ubuntu3) ... 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-15122929 armhf cosmic-proposed -c chroot:build-PACKAGEBUILD-15122929 --arch=armhf --dist=cosmic-proposed --nolog clustalw_2.1+lgpl-6.dsc Initiating build PACKAGEBUILD-15122929 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:52:48 UTC 2018 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-038.buildd +==============================================================================+ | clustalw 2.1+lgpl-6 (armhf) 14 Jul 2018 23:10 | +==============================================================================+ Package: clustalw Version: 2.1+lgpl-6 Source Version: 2.1+lgpl-6 Distribution: cosmic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/clustalw-U56DLy/clustalw-2.1+lgpl' with '<>' I: NOTICE: Log filtering will replace 'build/clustalw-U56DLy' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15122929/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-De1Rcg/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-De1Rcg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-De1Rcg/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-De1Rcg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-De1Rcg/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-De1Rcg/apt_archive ./ Packages [527 B] Fetched 2860 B in 49710d 6h 28min 15s (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-De1Rcg/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 49710d 6h 28min 15s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12442 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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-QSzSXn/apt_archive/sbuild-build-depends-clustalw-dummy.deb'. Ign:1 copy:/<>/resolver-QSzSXn/apt_archive ./ InRelease Get:2 copy:/<>/resolver-QSzSXn/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-QSzSXn/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-QSzSXn/apt_archive ./ Sources [211 B] Get:5 copy:/<>/resolver-QSzSXn/apt_archive ./ Packages [529 B] Fetched 2859 B in 0s (137 kB/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 15.9 MB of archives. After this operation, 57.7 MB of additional disk space will be used. Get:1 copy:/<>/resolver-QSzSXn/apt_archive ./ sbuild-build-depends-clustalw-dummy 0.invalid.0 [856 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main armhf libbsd0 armhf 0.9.1-1 [43.1 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main armhf bsdmainutils armhf 11.1.2ubuntu2 [176 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main armhf groff-base armhf 1.22.3-10 [1013 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main armhf libpipeline1 armhf 1.5.0-1 [21.1 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main armhf man-db armhf 2.8.3-2 [993 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main armhf libmagic-mgc armhf 1:5.33-3 [192 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main armhf libmagic1 armhf 1:5.33-3 [63.7 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main armhf file armhf 1:5.33-3 [22.1 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main armhf libelf1 armhf 0.170-0.5 [42.2 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main armhf libglib2.0-0 armhf 2.56.1-2ubuntu1 [1014 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main armhf libicu60 armhf 60.2-6ubuntu1 [7801 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libxml2 armhf 2.9.4+dfsg1-7build1 [568 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main armhf gettext-base armhf 0.19.8.1-6build1 [46.2 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main armhf m4 armhf 1.4.18-1 [181 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main armhf autoconf all 2.69-11 [322 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main armhf automake all 1:1.15.1-3ubuntu2 [509 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main armhf autopoint all 0.19.8.1-6build1 [412 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main armhf libtool all 2.4.6-2.1 [195 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-autoreconf all 19 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main armhf libarchive-zip-perl all 1.60-1ubuntu1 [84.6 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main armhf libfile-stripnondeterminism-perl all 0.042-1 [15.2 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-strip-nondeterminism all 0.042-1 [5188 B] Get:27 http://ftpmaster.internal/ubuntu cosmic/main armhf dwz armhf 0.12-2 [72.0 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main armhf libcroco3 armhf 0.6.12-2 [69.4 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main armhf gettext armhf 0.19.8.1-6build1 [834 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main armhf po-debconf all 1.0.20 [232 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main armhf debhelper all 11.3.2ubuntu1 [883 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.9 MB in 0s (1331 MB/s) Selecting previously unselected package libbsd0:armhf. (Reading database ... 12442 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_armhf.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_armhf.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.0-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.3-2_armhf.deb ... Unpacking man-db (2.8.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.33-3_armhf.deb ... Unpacking libmagic-mgc (1:5.33-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../06-libmagic1_1%3a5.33-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.33-3) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.33-3_armhf.deb ... Unpacking file (1:5.33-3) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../08-libelf1_0.170-0.5_armhf.deb ... Unpacking libelf1:armhf (0.170-0.5) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../09-libglib2.0-0_2.56.1-2ubuntu1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.56.1-2ubuntu1) ... Selecting previously unselected package libicu60:armhf. Preparing to unpack .../10-libicu60_60.2-6ubuntu1_armhf.deb ... Unpacking libicu60:armhf (60.2-6ubuntu1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../11-libxml2_2.9.4+dfsg1-7build1_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7build1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../12-gettext-base_0.19.8.1-6build1_armhf.deb ... Unpacking gettext-base (0.19.8.1-6build1) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../13-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.18-1_armhf.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../16-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../17-automake_1%3a1.15.1-3ubuntu2_all.deb ... Unpacking automake (1:1.15.1-3ubuntu2) ... Selecting previously unselected package autopoint. Preparing to unpack .../18-autopoint_0.19.8.1-6build1_all.deb ... Unpacking autopoint (0.19.8.1-6build1) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.6-2.1_all.deb ... Unpacking libtool (2.4.6-2.1) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.60-1ubuntu1_all.deb ... Unpacking libarchive-zip-perl (1.60-1ubuntu1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_0.042-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.042-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../23-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../24-dh-strip-nondeterminism_0.042-1_all.deb ... Unpacking dh-strip-nondeterminism (0.042-1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.12-2_armhf.deb ... Unpacking dwz (0.12-2) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../26-libcroco3_0.6.12-2_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.19.8.1-6build1_armhf.deb ... Unpacking gettext (0.19.8.1-6build1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_11.3.2ubuntu1_all.deb ... 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_armhf.deb ... Unpacking sbuild-build-depends-clustalw-dummy (0.invalid.0) ... Setting up libicu60:armhf (60.2-6ubuntu1) ... Setting up libarchive-zip-perl (1.60-1ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libelf1:armhf (0.170-0.5) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:armhf (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-6build1) ... Setting up libpipeline1:armhf (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:armhf (0.9.1-1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7build1) ... Setting up libmagic-mgc (1:5.33-3) ... Setting up libmagic1:armhf (1:5.33-3) ... Setting up libcroco3:armhf (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 4.4.0-130-generic arm64 (armv7l) 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-arm-linux-gnueabihf_2.30-22ubuntu1 binutils-common_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 libjson-c3_0.12.1-1.3 libkmod2_25-1ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 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 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 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 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-15122929 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15122929 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15122929 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 armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a 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 -a ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking target system type... arm-unknown-linux-gnueabihf building for linux-gnueabihf 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 -a 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/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 ./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 ./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 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/../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; ^~~~~~~~ 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/../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"); ^~~~~~~~~~~~~~ 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 ./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/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 /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/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 ./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/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 /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; ^~~~~~~~ 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: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 In file included from /usr/include/c++/7/vector:69:0, from ./tree/NJTree.h:9, from ./tree/NJTree.cpp:10: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ 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 /usr/include/c++/7/vector:64:0, from ./tree/NJTree.h:9, from ./tree/NJTree.cpp:10: /usr/include/c++/7/bits/stl_vector.h: In member function ‘virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)’: /usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/../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: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; ^~~~~~~~ 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"); ^~~~~~~~~~~~~~ ./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 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 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"); ^~~~~~~~~~~~~~ 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 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 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 ./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; ^~~~~~~~ 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"); ^~~~~~~~~~~~~~ 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 ./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 VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp In file included from /usr/include/c++/7/algorithm:62:0, from ./general/Utility.cpp:18: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ./general/Utility.cpp:18: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ 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 In file included from /usr/include/c++/7/algorithm:62:0, from ./general/Utility.cpp:18: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘double clustalw::Utility::median(std::vector)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 /usr/include/c++/7/vector:69:0, from ./general/../alignment/Alignment.h:36, from ./general/Stats.cpp:15: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘void clustalw::Stats::logInputSeqStats(clustalw::Alignment*)’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -a 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-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a 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 -a 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 -a dh_installman -a dh_installmenu -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a 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_armhf.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_armhf.deb'. Renaming clustalw-dbgsym_2.1+lgpl-6_armhf.deb to clustalw-dbgsym_2.1+lgpl-6_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../clustalw_2.1+lgpl-6_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not 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_armhf.changes: ---------------------------------- Format: 1.8 Date: Sat, 14 Jul 2018 17:09:36 +0200 Source: clustalw Binary: clustalw Architecture: armhf 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: 6d49e590443300c15dcb3d44b300f6c16d22375d 3157204 clustalw-dbgsym_2.1+lgpl-6_armhf.ddeb 26db7ec0d9ccfc87b82501c24e9465a2d07afdd9 4864 clustalw_2.1+lgpl-6_armhf.buildinfo c77f7c9ebd252d92eae9c8059f2c52ef60fc0ca6 242472 clustalw_2.1+lgpl-6_armhf.deb Checksums-Sha256: aacea4113196b0e25edfb429630e6c11a2502d0a9159aff1a6112bf6b3c862b7 3157204 clustalw-dbgsym_2.1+lgpl-6_armhf.ddeb d168dabdc2984963d9674520f23db495dfb86fac5a0edd180f372c7b038daf92 4864 clustalw_2.1+lgpl-6_armhf.buildinfo 23c19e1838f36a48031b4933850be6006411809c4a752e6344cb19ccd2333129 242472 clustalw_2.1+lgpl-6_armhf.deb Files: c6030214937308575ed235f11e236950 3157204 debug optional clustalw-dbgsym_2.1+lgpl-6_armhf.ddeb 386b1ae3a5c62860702532b09f30530c 4864 science optional clustalw_2.1+lgpl-6_armhf.buildinfo 5bcbde3f9615e344a4e1a09ed8db37eb 242472 science optional clustalw_2.1+lgpl-6_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ clustalw_2.1+lgpl-6_armhf.deb ----------------------------- new debian package, version 2.0. size 242472 bytes: control archive=1496 bytes. 1172 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: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 522 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), 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 458884 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: armhf Build-Space: 37484 Build-Time: 76 Distribution: cosmic-proposed Host Architecture: armhf Install-Time: 17 Job: clustalw_2.1+lgpl-6.dsc Machine Architecture: arm64 Package: clustalw Package-Time: 94 Source-Version: 2.1+lgpl-6 Space: 37484 Status: successful Version: 2.1+lgpl-6 -------------------------------------------------------------------------------- Finished at 20180714-2311 Build needed 00:01:34, 37484k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15122929 Scanning for processes to kill in build PACKAGEBUILD-15122929