RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-035 4.4.0-97-generic #120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_154 python-lpbuildd_154 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_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 3 Nov 11:25:40 ntpdate[1802]: adjust time server 10.211.37.1 offset 0.002039 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13653816 /home/buildd/filecache-default/f027e517e95d0e91684230ee23be60d709f816c0 Creating target for build PACKAGEBUILD-13653816 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13653816 Starting target for build PACKAGEBUILD-13653816 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13653816 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-13653816 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13653816 Updating target for build PACKAGEBUILD-13653816 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed InRelease [85.4 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main amd64 Packages [1064 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [541 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/restricted amd64 Packages [8848 B] Get:8 http://ftpmaster.internal/ubuntu bionic/restricted Translation-en [2788 B] Get:9 http://ftpmaster.internal/ubuntu bionic/universe amd64 Packages [8153 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4817 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/multiverse amd64 Packages [150 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/multiverse Translation-en [109 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 Packages [121 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [73.0 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 Packages [665 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [496 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-proposed/multiverse amd64 Packages [3500 B] Get:18 http://ftpmaster.internal/ubuntu bionic-proposed/multiverse Translation-en [6732 B] Fetched 16.7 MB in 6s (2605 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: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libustr-1.0-1 libwind0-heimdal Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: apt-transport-https* The following packages will be upgraded: apt base-files base-passwd binutils binutils-common binutils-x86-64-linux-gnu build-essential coreutils cpp-7 debconf dpkg dpkg-dev e2fslibs e2fsprogs g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdpkg-perl libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed4 libitm1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblsan0 libmpx2 libnettle6 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libss2 libstdc++-7-dev libstdc++6 libsystemd0 libtsan0 libubsan0 libudev1 linux-libc-dev multiarch-support perl perl-base perl-modules-5.26 pinentry-curses systemd systemd-sysv sysvinit-utils tzdata 80 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. Need to get 58.1 MB of archives. After this operation, 452 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main amd64 base-files amd64 10ubuntu1 [55.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main amd64 coreutils amd64 8.26-3ubuntu4 [1213 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main amd64 dpkg amd64 1.19.0.4ubuntu1 [1145 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main amd64 libc6-dev amd64 2.26-0ubuntu2 [2524 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main amd64 libc-dev-bin amd64 2.26-0ubuntu2 [69.6 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main amd64 linux-libc-dev amd64 4.13.0-16.19 [954 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main amd64 libquadmath0 amd64 7.2.0-12ubuntu1 [132 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main amd64 libitm1 amd64 7.2.0-12ubuntu1 [27.6 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main amd64 gcc-7-base amd64 7.2.0-12ubuntu1 [18.3 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main amd64 libgcc1 amd64 1:7.2.0-12ubuntu1 [39.3 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main amd64 libmpx2 amd64 7.2.0-12ubuntu1 [11.7 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main amd64 libgomp1 amd64 7.2.0-12ubuntu1 [76.4 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main amd64 libatomic1 amd64 7.2.0-12ubuntu1 [8954 B] Get:14 http://ftpmaster.internal/ubuntu bionic/main amd64 libasan4 amd64 7.2.0-12ubuntu1 [360 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main amd64 liblsan0 amd64 7.2.0-12ubuntu1 [133 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main amd64 libtsan0 amd64 7.2.0-12ubuntu1 [282 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main amd64 libubsan0 amd64 7.2.0-12ubuntu1 [126 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main amd64 libcilkrts5 amd64 7.2.0-12ubuntu1 [42.5 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main amd64 cpp-7 amd64 7.2.0-12ubuntu1 [6728 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main amd64 libcc1-0 amd64 7.2.0-12ubuntu1 [38.7 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main amd64 g++-7 amd64 7.2.0-12ubuntu1 [7554 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main amd64 gcc-7 amd64 7.2.0-12ubuntu1 [7414 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main amd64 libgcc-7-dev amd64 7.2.0-12ubuntu1 [2377 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main amd64 libstdc++-7-dev amd64 7.2.0-12ubuntu1 [1457 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main amd64 libstdc++6 amd64 7.2.0-12ubuntu1 [405 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1.1 [241 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main amd64 libbinutils amd64 2.29.1-6ubuntu1 [502 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main amd64 binutils amd64 2.29.1-6ubuntu1 [3344 B] Get:29 http://ftpmaster.internal/ubuntu bionic/main amd64 binutils-common amd64 2.29.1-6ubuntu1 [190 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main amd64 binutils-x86-64-linux-gnu amd64 2.29.1-6ubuntu1 [1825 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main amd64 libc6 amd64 2.26-0ubuntu2 [2778 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 e2fslibs amd64 1.43.7-1 [157 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 e2fsprogs amd64 1.43.7-1 [498 kB] Get:34 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 perl-modules-5.26 all 5.26.1-2ubuntu1 [2760 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libperl5.26 amd64 5.26.1-2ubuntu1 [3535 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 perl amd64 5.26.1-2ubuntu1 [201 kB] Get:37 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 perl-base amd64 5.26.1-2ubuntu1 [1389 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main amd64 base-passwd amd64 3.5.44 [47.2 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main amd64 libc-bin amd64 2.26-0ubuntu2 [593 kB] Get:40 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 sysvinit-utils amd64 2.88dsf-59.10ubuntu1 [18.6 kB] Get:41 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libudev1 amd64 235-2ubuntu1 [54.5 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libapt-pkg5.0 amd64 1.6~alpha3 [779 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libgpg-error0 amd64 1.27-4 [36.8 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main amd64 libgcrypt20 amd64 1.7.9-1 [400 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main amd64 gpgv amd64 2.1.15-1ubuntu8 [186 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main amd64 libseccomp2 amd64 2.3.1-2.1ubuntu3 [37.3 kB] Get:47 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 apt amd64 1.6~alpha3 [1144 kB] Get:48 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 debconf all 1.5.64 [124 kB] Get:49 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libapparmor1 amd64 2.11.0-2ubuntu18 [28.8 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main amd64 libcap2 amd64 1:2.25-1.1 [13.2 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main amd64 libpcre3 amd64 2:8.39-5ubuntu3 [229 kB] Get:52 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libselinux1 amd64 2.7-2 [68.3 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 systemd amd64 235-2ubuntu1 [2832 kB] Get:54 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libsystemd0 amd64 235-2ubuntu1 [196 kB] Get:55 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 systemd-sysv amd64 235-2ubuntu1 [12.7 kB] Get:56 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libcap-ng0 amd64 0.7.7-3.1 [11.1 kB] Get:57 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libcomerr2 amd64 1.43.7-1 [11.4 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main amd64 libsemanage-common all 2.7-2 [6916 B] Get:59 http://ftpmaster.internal/ubuntu bionic/main amd64 libsemanage1 amd64 2.7-2 [84.6 kB] Get:60 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libss2 amd64 1.43.7-1 [11.1 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main amd64 libnettle6 amd64 3.3-2 [91.7 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main amd64 libhogweed4 amd64 3.3-2 [135 kB] Get:63 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libp11-kit0 amd64 0.23.9-2 [187 kB] Get:64 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 pinentry-curses amd64 1.0.0-3 [34.7 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main amd64 gnupg amd64 2.1.15-1ubuntu8 [780 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main amd64 gnupg-agent amd64 2.1.15-1ubuntu8 [255 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main amd64 libsqlite3-0 amd64 3.20.1-2 [491 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main amd64 multiarch-support amd64 2.26-0ubuntu2 [6832 B] Get:69 http://ftpmaster.internal/ubuntu bionic/main amd64 tzdata all 2017c-1 [188 kB] Get:70 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libgssapi-krb5-2 amd64 1.15.2-2 [121 kB] Get:71 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libkrb5-3 amd64 1.15.2-2 [278 kB] Get:72 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libkrb5support0 amd64 1.15.2-2 [31.5 kB] Get:73 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libk5crypto3 amd64 1.15.2-2 [85.4 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main amd64 libkeyutils1 amd64 1.5.9-9.1ubuntu1 [9488 B] Get:75 http://ftpmaster.internal/ubuntu bionic/main amd64 libpng16-16 amd64 1.6.34-1 [176 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main amd64 dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main amd64 libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main amd64 build-essential amd64 12.4ubuntu1 [4758 B] Get:79 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libpsl5 amd64 0.18.0-4 [40.7 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main amd64 libcurl3-gnutls amd64 7.55.1-1ubuntu2.1 [193 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.1 MB in 1s (29.4 MB/s) (Reading database ... 12676 files and directories currently installed.) 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Current default time zone: 'Etc/UTC' Local time is now: Fri Nov 3 11:26:45 UTC 2017. Universal Time is now: Fri Nov 3 11:26:45 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (235-2ubuntu1) ... Setting up libubsan0:amd64 (7.2.0-12ubuntu1) ... Setting up libtsan0:amd64 (7.2.0-12ubuntu1) ... Setting up linux-libc-dev:amd64 (4.13.0-16.19) ... Setting up perl-modules-5.26 (5.26.1-2ubuntu1) ... Setting up libkrb5support0:amd64 (1.15.2-2) ... Setting up cpp-7 (7.2.0-12ubuntu1) ... Setting up liblsan0:amd64 (7.2.0-12ubuntu1) ... Setting up binutils-common:amd64 (2.29.1-6ubuntu1) ... Setting up libmpx2:amd64 (7.2.0-12ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up libperl5.26:amd64 (5.26.1-2ubuntu1) ... Setting up libsqlite3-0:amd64 (3.20.1-2) ... Setting up pinentry-curses (1.0.0-3) ... Setting up libc-dev-bin (2.26-0ubuntu2) ... Setting up libkeyutils1:amd64 (1.5.9-9.1ubuntu1) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13653816 amd64 bionic-proposed -c chroot:build-PACKAGEBUILD-13653816 --arch=amd64 --dist=bionic-proposed --nolog -A clustalx_2.1+lgpl-6.dsc Initiating build PACKAGEBUILD-13653816 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-97-generic #120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-035.buildd +==============================================================================+ | clustalx 2.1+lgpl-6 (amd64) 03 Nov 2017 11:26 | +==============================================================================+ Package: clustalx Version: 2.1+lgpl-6 Source Version: 2.1+lgpl-6 Distribution: bionic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/clustalx-GpEqLJ/clustalx-2.1+lgpl' with '<>' I: NOTICE: Log filtering will replace 'build/clustalx-GpEqLJ' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13653816/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- clustalx_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-pISdQl/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-pISdQl/apt_archive ./ InRelease Get:2 copy:/<>/resolver-pISdQl/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-pISdQl/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-pISdQl/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-pISdQl/apt_archive ./ Packages [524 B] Fetched 2857 B in 0s (21.7 kB/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: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libustr-1.0-1 libwind0-heimdal 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-pISdQl/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (44.2 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12671 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), qtbase5-dev, qtbase5-dev-tools, qttools5-dev-tools Filtered Build-Depends: debhelper (>= 9), qtbase5-dev, qtbase5-dev-tools, qttools5-dev-tools dpkg-deb: building package 'sbuild-build-depends-clustalx-dummy' in '/<>/resolver-FpAnEr/apt_archive/sbuild-build-depends-clustalx-dummy.deb'. Ign:1 copy:/<>/resolver-FpAnEr/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FpAnEr/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-FpAnEr/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FpAnEr/apt_archive ./ Sources [229 B] Get:5 copy:/<>/resolver-FpAnEr/apt_archive ./ Packages [549 B] Fetched 2897 B in 0s (72.2 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install clustalx 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: libasn1-8-heimdal libcurl3-gnutls libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libkrb5-26-heimdal libldap-2.4-2 libldap-common libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libustr-1.0-1 libwind0-heimdal 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 file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian iso-codes libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libboost-filesystem1.65.1 libboost-system1.65.1 libbsd0 libcap2-bin libcapnp-0.6.1 libcroco3 libcups2 libdbus-1-3 libdouble-conversion1 libdrm-amdgpu1 libdrm-common libdrm-dev libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl1-mesa libegl1-mesa-dev libelf1 libevdev2 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgbm1 libgl1-mesa-dev libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libgles2-mesa libgles2-mesa-dev libglib2.0-0 libglu1-mesa libglu1-mesa-dev libgraphite2-3 libgstreamer-plugins-base1.0-0 libgstreamer1.0-0 libgudev-1.0-0 libharfbuzz0b libhyphen0 libice6 libicu59 libinput-bin libinput10 libjpeg-turbo8 libjpeg8 libllvm5.0 libmagic-mgc libmagic1 libmirclient-dev libmirclient9 libmircommon-dev libmircommon7 libmircookie-dev libmircookie2 libmircore-dev libmircore1 libmirprotobuf3 libmtdev1 liborc-0.4-0 libpciaccess0 libpipeline1 libprotobuf-dev libprotobuf-lite10 libprotobuf10 libpthread-stubs0-dev libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5designer5 libqt5designercomponents5 libqt5gui5 libqt5help5 libqt5network5 libqt5positioning5 libqt5printsupport5 libqt5qml5 libqt5quick5 libqt5quickwidgets5 libqt5sensors5 libqt5sql5 libqt5test5 libqt5webchannel5 libqt5webkit5 libqt5widgets5 libqt5xml5 libsensors4 libsigsegv2 libsm6 libtimedate-perl libtool libwacom-common libwacom2 libwayland-bin libwayland-client0 libwayland-cursor0 libwayland-dev libwayland-egl1-mesa libwayland-server0 libwebp6 libx11-6 libx11-data libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render-util0 libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-shm0 libxcb-sync-dev libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb-xinerama0 libxcb-xkb1 libxcb1 libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3 libxi6 libxkbcommon-dev libxkbcommon-x11-0 libxkbcommon0 libxml2 libxshmfence-dev libxshmfence1 libxslt1.1 libxxf86vm-dev libxxf86vm1 m4 man-db mesa-common-dev po-debconf qt5-qmake qt5-qmake-bin qtbase5-dev qtbase5-dev-tools qtchooser qttools5-dev-tools ucf x11-common x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev x11proto-xf86vidmode-dev xkb-data xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff isoquery cups-common libvisual-0.4-plugins gstreamer1.0-tools pciutils libthai0 qt5-image-formats-plugins qtwayland5 qt5-qmltooling-plugins lm-sensors libtool-doc gfortran | fortran95-compiler gcj-jdk libxcb-doc libxext-doc m4-doc less www-browser libmail-box-perl default-libmysqlclient-dev firebird-dev libpq-dev libsqlite3-dev unixodbc-dev Recommended packages: curl | wget | lynx-cur libpam-cap dbus libarchive-cpio-perl libtxc-dxtn-s2tc | libtxc-dxtn-s2tc0 | libtxc-dxtn0 libglib2.0-data shared-mime-info xdg-user-dirs gstreamer1.0-plugins-base qttranslations5-l10n libqt5svg5 qt5-gtk-platformtheme geoclue-2.0 libqt5sql5-sqlite | libqt5sql5-mysql | libqt5sql5-odbc | libqt5sql5-psql | libqt5sql5-tds | libqt5sql5-ibase libltdl-dev libwacom-bin libx11-doc libmail-sendmail-perl libqt5opengl5-dev libqt5sql5-sqlite The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian iso-codes libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libboost-filesystem1.65.1 libboost-system1.65.1 libbsd0 libcap2-bin libcapnp-0.6.1 libcroco3 libcups2 libdbus-1-3 libdouble-conversion1 libdrm-amdgpu1 libdrm-common libdrm-dev libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl1-mesa libegl1-mesa-dev libelf1 libevdev2 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgbm1 libgl1-mesa-dev libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libgles2-mesa libgles2-mesa-dev libglib2.0-0 libglu1-mesa libglu1-mesa-dev libgraphite2-3 libgstreamer-plugins-base1.0-0 libgstreamer1.0-0 libgudev-1.0-0 libharfbuzz0b libhyphen0 libice6 libicu59 libinput-bin libinput10 libjpeg-turbo8 libjpeg8 libllvm5.0 libmagic-mgc libmagic1 libmirclient-dev libmirclient9 libmircommon-dev libmircommon7 libmircookie-dev libmircookie2 libmircore-dev libmircore1 libmirprotobuf3 libmtdev1 liborc-0.4-0 libpciaccess0 libpipeline1 libprotobuf-dev libprotobuf-lite10 libprotobuf10 libpthread-stubs0-dev libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5designer5 libqt5designercomponents5 libqt5gui5 libqt5help5 libqt5network5 libqt5positioning5 libqt5printsupport5 libqt5qml5 libqt5quick5 libqt5quickwidgets5 libqt5sensors5 libqt5sql5 libqt5test5 libqt5webchannel5 libqt5webkit5 libqt5widgets5 libqt5xml5 libsensors4 libsigsegv2 libsm6 libtimedate-perl libtool libwacom-common libwacom2 libwayland-bin libwayland-client0 libwayland-cursor0 libwayland-dev libwayland-egl1-mesa libwayland-server0 libwebp6 libx11-6 libx11-data libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render-util0 libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-shm0 libxcb-sync-dev libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb-xinerama0 libxcb-xkb1 libxcb1 libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3 libxi6 libxkbcommon-dev libxkbcommon-x11-0 libxkbcommon0 libxml2 libxshmfence-dev libxshmfence1 libxslt1.1 libxxf86vm-dev libxxf86vm1 m4 man-db mesa-common-dev po-debconf qt5-qmake qt5-qmake-bin qtbase5-dev qtbase5-dev-tools qtchooser qttools5-dev-tools sbuild-build-depends-clustalx-dummy ucf x11-common x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev x11proto-xf86vidmode-dev xkb-data xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 201 newly installed, 1 to remove and 0 not upgraded. Need to get 83.7 MB of archives. After this operation, 458 MB of additional disk space will be used. Get:1 copy:/<>/resolver-FpAnEr/apt_archive ./ sbuild-build-depends-clustalx-dummy 0.invalid.0 [876 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] Get:3 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libbsd0 amd64 0.8.6-2 [41.8 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main amd64 libxdmcp6 amd64 1:1.1.2-3 [10.7 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb1 amd64 1.12-1ubuntu1 [45.2 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main amd64 libx11-data all 2:1.6.4-3 [114 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main amd64 libx11-6 amd64 2:1.6.4-3 [572 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main amd64 groff-base amd64 1.22.3-9 [1144 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main amd64 bsdmainutils amd64 9.0.12+nmu1ubuntu1 [179 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main amd64 libpipeline1 amd64 1.4.2-1 [25.2 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main amd64 man-db amd64 2.7.6.1-2 [895 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main amd64 libexpat1 amd64 2.2.3-1 [72.3 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main amd64 libfreetype6 amd64 2.8-0.2ubuntu2 [333 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main amd64 ucf all 3.0036 [52.9 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main amd64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main amd64 fontconfig-config all 2.12.6-0ubuntu1 [55.5 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main amd64 libfontconfig1 amd64 2.12.6-0ubuntu1 [136 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main amd64 fontconfig amd64 2.12.6-0ubuntu1 [169 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main amd64 libjpeg-turbo8 amd64 1.5.2-0ubuntu5 [110 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main amd64 libmtdev1 amd64 1.1.5-1ubuntu2 [13.8 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main amd64 libglib2.0-0 amd64 2.54.1-1ubuntu1 [1163 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main amd64 libcap2-bin amd64 1:2.25-1.1 [20.5 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main amd64 libgstreamer1.0-0 amd64 1.12.3-1 [818 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main amd64 liborc-0.4-0 amd64 1:0.4.27-1 [138 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 iso-codes all 3.76-1 [2320 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main amd64 libgstreamer-plugins-base1.0-0 amd64 1.12.3-1 [654 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main amd64 libhyphen0 amd64 2.8.8-5 [26.5 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main amd64 libicu59 amd64 59.1-3ubuntu1 [7815 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:31 http://ftpmaster.internal/ubuntu bionic/main amd64 libdouble-conversion1 amd64 2.0.1-4ubuntu1 [33.0 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5core5a amd64 5.9.2+dfsg-4ubuntu5 [2033 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libdrm-common all 2.4.85-1 [4788 B] Get:34 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libdrm2 amd64 2.4.85-1 [30.5 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main amd64 libwayland-client0 amd64 1.14.0-1 [22.4 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main amd64 libwayland-server0 amd64 1.14.0-1 [28.5 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main amd64 libgbm1 amd64 17.2.2-0ubuntu1 [24.3 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main amd64 libboost-system1.65.1 amd64 1.65.1+dfsg-0ubuntu2 [10.6 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main amd64 libcapnp-0.6.1 amd64 0.6.1-1 [657 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main amd64 libboost-filesystem1.65.1 amd64 1.65.1+dfsg-0ubuntu2 [40.2 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main amd64 libmircore1 amd64 0.28.1+18.04.20171030-0ubuntu1 [30.2 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main amd64 libmircommon7 amd64 0.28.1+18.04.20171030-0ubuntu1 [73.9 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main amd64 libprotobuf-lite10 amd64 3.0.0-9ubuntu5 [97.1 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main amd64 libmirprotobuf3 amd64 0.28.1+18.04.20171030-0ubuntu1 [129 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main amd64 xkb-data all 2.19-1.1ubuntu1 [312 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main amd64 libxkbcommon0 amd64 0.7.1-2 [97.2 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main amd64 libmirclient9 amd64 0.28.1+18.04.20171030-0ubuntu1 [199 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main amd64 libx11-xcb1 amd64 2:1.6.4-3 [9626 B] Get:49 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-dri2-0 amd64 1.12-1ubuntu1 [6838 B] Get:50 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-dri3-0 amd64 1.12-1ubuntu1 [5156 B] Get:51 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-present0 amd64 1.12-1ubuntu1 [5436 B] Get:52 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-sync1 amd64 1.12-1ubuntu1 [8746 B] Get:53 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-xfixes0 amd64 1.12-1ubuntu1 [9292 B] Get:54 http://ftpmaster.internal/ubuntu bionic/main amd64 libxshmfence1 amd64 1.2-1 [5042 B] Get:55 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libdrm-amdgpu1 amd64 2.4.85-1 [19.1 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main amd64 libpciaccess0 amd64 0.13.4-1ubuntu1 [17.9 kB] Get:57 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libdrm-intel1 amd64 2.4.85-1 [59.8 kB] Get:58 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libdrm-nouveau2 amd64 2.4.85-1 [16.5 kB] Get:59 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libdrm-radeon1 amd64 2.4.85-1 [21.7 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main amd64 libelf1 amd64 0.170-0.1 [44.3 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main amd64 libglapi-mesa amd64 17.2.2-0ubuntu1 [22.3 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main amd64 libedit2 amd64 3.1-20170329-1 [76.9 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main amd64 libllvm5.0 amd64 1:5.0-4 [13.7 MB] Get:64 http://ftpmaster.internal/ubuntu bionic/main amd64 libsensors4 amd64 1:3.4.0-4 [28.8 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main amd64 libgl1-mesa-dri amd64 17.2.2-0ubuntu1 [5709 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main amd64 libegl1-mesa amd64 17.2.2-0ubuntu1 [85.0 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-glx0 amd64 1.12-1ubuntu1 [22.3 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main amd64 libxdamage1 amd64 1:1.1.4-3 [6934 B] Get:69 http://ftpmaster.internal/ubuntu bionic/main amd64 libxfixes3 amd64 1:5.0.3-1 [10.8 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main amd64 libxxf86vm1 amd64 1:1.1.4-1 [10.6 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main amd64 libgl1-mesa-glx amd64 17.2.2-0ubuntu1 [130 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main amd64 libgraphite2-3 amd64 1.3.10-6 [77.7 kB] Get:73 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libharfbuzz0b amd64 1.6.2-1 [224 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main amd64 x11-common all 1:7.7+19ubuntu3 [22.0 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main amd64 libice6 amd64 2:1.0.9-2 [40.2 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main amd64 libevdev2 amd64 1.5.7+dfsg-1 [28.8 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main amd64 libgudev-1.0-0 amd64 1:232-1 [13.3 kB] Get:78 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libwacom-common all 0.26-1 [34.7 kB] Get:79 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libwacom2 amd64 0.26-1 [17.1 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main amd64 libinput-bin amd64 1.8.2-1ubuntu2 [9902 B] Get:81 http://ftpmaster.internal/ubuntu bionic/main amd64 libinput10 amd64 1.8.2-1ubuntu2 [78.1 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main amd64 libdbus-1-3 amd64 1.12.0-1ubuntu1 [174 kB] Get:83 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5dbus5 amd64 5.9.2+dfsg-4ubuntu5 [195 kB] Get:84 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5network5 amd64 5.9.2+dfsg-4ubuntu5 [633 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-icccm4 amd64 0.4.1-1ubuntu1 [10.4 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-shm0 amd64 1.12-1ubuntu1 [5482 B] Get:88 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-util1 amd64 0.4.0-0ubuntu3 [11.2 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-image0 amd64 0.4.0-1build1 [12.3 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-keysyms1 amd64 0.4.0-1 [8406 B] Get:91 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-randr0 amd64 1.12-1ubuntu1 [16.0 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-render0 amd64 1.12-1ubuntu1 [14.8 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-render-util0 amd64 0.3.9-1 [9638 B] Get:94 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-shape0 amd64 1.12-1ubuntu1 [5864 B] Get:95 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-xinerama0 amd64 1.12-1ubuntu1 [5156 B] Get:96 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-xkb1 amd64 1.12-1ubuntu1 [30.2 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/main amd64 libxi6 amd64 2:1.7.9-1 [29.2 kB] Get:98 http://ftpmaster.internal/ubuntu bionic/main amd64 libxkbcommon-x11-0 amd64 0.7.1-2 [13.3 kB] Get:99 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5gui5 amd64 5.9.2+dfsg-4ubuntu5 [2567 kB] Get:100 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5positioning5 amd64 5.9.2+dfsg-2build1 [130 kB] Get:101 http://ftpmaster.internal/ubuntu bionic/main amd64 libavahi-common-data amd64 0.6.32-1ubuntu1 [22.0 kB] Get:102 http://ftpmaster.internal/ubuntu bionic/main amd64 libavahi-common3 amd64 0.6.32-1ubuntu1 [21.6 kB] Get:103 http://ftpmaster.internal/ubuntu bionic/main amd64 libavahi-client3 amd64 0.6.32-1ubuntu1 [25.1 kB] Get:104 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libcups2 amd64 2.2.6-1 [210 kB] Get:105 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5widgets5 amd64 5.9.2+dfsg-4ubuntu5 [2200 kB] Get:106 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5printsupport5 amd64 5.9.2+dfsg-4ubuntu5 [178 kB] Get:107 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5qml5 amd64 5.9.2-3ubuntu1 [1237 kB] Get:108 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5quick5 amd64 5.9.2-3ubuntu1 [1197 kB] Get:109 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5sensors5 amd64 5.9.2-2build1 [114 kB] Get:110 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5webchannel5 amd64 5.9.2-2 [47.7 kB] Get:111 http://ftpmaster.internal/ubuntu bionic/main amd64 libwebp6 amd64 0.6.0-3 [181 kB] Get:112 http://ftpmaster.internal/ubuntu bionic/main amd64 libxml2 amd64 2.9.4+dfsg1-5ubuntu1 [669 kB] Get:113 http://ftpmaster.internal/ubuntu bionic/main amd64 libxslt1.1 amd64 1.1.29-2.1ubuntu1 [149 kB] Get:114 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5webkit5 amd64 5.212.0~alpha2-5 [11.8 MB] Get:115 http://ftpmaster.internal/ubuntu bionic/main amd64 libmagic-mgc amd64 1:5.32-1 [184 kB] Get:116 http://ftpmaster.internal/ubuntu bionic/main amd64 libmagic1 amd64 1:5.32-1 [68.4 kB] Get:117 http://ftpmaster.internal/ubuntu bionic/main amd64 file amd64 1:5.32-1 [22.0 kB] Get:118 http://ftpmaster.internal/ubuntu bionic/main amd64 gettext-base amd64 0.19.8.1-4ubuntu1 [49.4 kB] Get:119 http://ftpmaster.internal/ubuntu bionic/main amd64 libsigsegv2 amd64 2.11-1 [13.2 kB] Get:120 http://ftpmaster.internal/ubuntu bionic/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:121 http://ftpmaster.internal/ubuntu bionic/main amd64 autoconf all 2.69-11 [322 kB] Get:122 http://ftpmaster.internal/ubuntu bionic/main amd64 autotools-dev all 20161112.1+nmu1 [40.2 kB] Get:123 http://ftpmaster.internal/ubuntu bionic/main amd64 automake all 1:1.15.1-3ubuntu1 [509 kB] Get:124 http://ftpmaster.internal/ubuntu bionic/main amd64 autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:125 http://ftpmaster.internal/ubuntu bionic/main amd64 libtool all 2.4.6-2 [194 kB] Get:126 http://ftpmaster.internal/ubuntu bionic/main amd64 dh-autoreconf all 14 [15.5 kB] Get:127 http://ftpmaster.internal/ubuntu bionic/main amd64 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:128 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:129 http://ftpmaster.internal/ubuntu bionic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:130 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 dh-strip-nondeterminism all 0.040-1 [5196 B] Get:131 http://ftpmaster.internal/ubuntu bionic/main amd64 libcroco3 amd64 0.6.12-1 [81.3 kB] Get:132 http://ftpmaster.internal/ubuntu bionic/main amd64 gettext amd64 0.19.8.1-4ubuntu1 [1093 kB] Get:133 http://ftpmaster.internal/ubuntu bionic/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:134 http://ftpmaster.internal/ubuntu bionic/main amd64 po-debconf all 1.0.20 [232 kB] Get:135 http://ftpmaster.internal/ubuntu bionic/main amd64 debhelper all 10.10.5ubuntu1 [876 kB] Get:136 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libdrm-dev amd64 2.4.85-1 [236 kB] Get:137 http://ftpmaster.internal/ubuntu bionic/main amd64 libwayland-egl1-mesa amd64 17.2.2-0ubuntu1 [5770 B] Get:138 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-dri2-dev all 2.8-2 [12.6 kB] Get:139 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-gl-dev all 1.4.17-1 [17.9 kB] Get:140 http://ftpmaster.internal/ubuntu bionic/main amd64 xorg-sgml-doctools all 1:1.11-1 [12.9 kB] Get:141 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-core-dev all 7.0.31-1 [700 kB] Get:142 http://ftpmaster.internal/ubuntu bionic/main amd64 libxau-dev amd64 1:1.0.8-1 [11.1 kB] Get:143 http://ftpmaster.internal/ubuntu bionic/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [25.1 kB] Get:144 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-input-dev all 2.3.2-1 [118 kB] Get:145 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-kb-dev all 1.0.7-1 [226 kB] Get:146 http://ftpmaster.internal/ubuntu bionic/main amd64 xtrans-dev all 1.3.5-1 [70.5 kB] Get:147 http://ftpmaster.internal/ubuntu bionic/main amd64 libpthread-stubs0-dev amd64 0.3-4 [4068 B] Get:148 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb1-dev amd64 1.12-1ubuntu1 [79.8 kB] Get:149 http://ftpmaster.internal/ubuntu bionic/main amd64 libx11-dev amd64 2:1.6.4-3 [642 kB] Get:150 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-xext-dev all 7.3.0-1 [212 kB] Get:151 http://ftpmaster.internal/ubuntu bionic/main amd64 libxext-dev amd64 2:1.3.3-1 [82.1 kB] Get:152 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-xf86vidmode-dev all 2.3.1-2 [6116 B] Get:153 http://ftpmaster.internal/ubuntu bionic/main amd64 libxxf86vm-dev amd64 1:1.1.4-1 [13.3 kB] Get:154 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-fixes-dev all 1:5.0-2ubuntu2 [14.2 kB] Get:155 http://ftpmaster.internal/ubuntu bionic/main amd64 libxfixes-dev amd64 1:5.0.3-1 [11.0 kB] Get:156 http://ftpmaster.internal/ubuntu bionic/main amd64 x11proto-damage-dev all 1:1.2.1-2 [8286 B] Get:157 http://ftpmaster.internal/ubuntu bionic/main amd64 libxdamage-dev amd64 1:1.1.4-3 [5028 B] Get:158 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-glx0-dev amd64 1.12-1ubuntu1 [27.5 kB] Get:159 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-dri2-0-dev amd64 1.12-1ubuntu1 [8376 B] Get:160 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-dri3-dev amd64 1.12-1ubuntu1 [5742 B] Get:161 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-render0-dev amd64 1.12-1ubuntu1 [18.3 kB] Get:162 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-randr0-dev amd64 1.12-1ubuntu1 [19.5 kB] Get:163 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-shape0-dev amd64 1.12-1ubuntu1 [7056 B] Get:164 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-xfixes0-dev amd64 1.12-1ubuntu1 [11.6 kB] Get:165 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-sync-dev amd64 1.12-1ubuntu1 [10.5 kB] Get:166 http://ftpmaster.internal/ubuntu bionic/main amd64 libxcb-present-dev amd64 1.12-1ubuntu1 [6868 B] Get:167 http://ftpmaster.internal/ubuntu bionic/main amd64 libxshmfence-dev amd64 1.2-1 [3676 B] Get:168 http://ftpmaster.internal/ubuntu bionic/main amd64 libx11-xcb-dev amd64 2:1.6.4-3 [9660 B] Get:169 http://ftpmaster.internal/ubuntu bionic/main amd64 libwayland-cursor0 amd64 1.14.0-1 [9898 B] Get:170 http://ftpmaster.internal/ubuntu bionic/main amd64 libwayland-bin amd64 1.14.0-1 [18.7 kB] Get:171 http://ftpmaster.internal/ubuntu bionic/main amd64 libwayland-dev amd64 1.14.0-1 [98.1 kB] Get:172 http://ftpmaster.internal/ubuntu bionic/main amd64 libmircore-dev amd64 0.28.1+18.04.20171030-0ubuntu1 [25.3 kB] Get:173 http://ftpmaster.internal/ubuntu bionic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-0ubuntu2 [176 kB] Get:174 http://ftpmaster.internal/ubuntu bionic/main amd64 libprotobuf10 amd64 3.0.0-9ubuntu5 [650 kB] Get:175 http://ftpmaster.internal/ubuntu bionic/main amd64 libprotobuf-dev amd64 3.0.0-9ubuntu5 [958 kB] Get:176 http://ftpmaster.internal/ubuntu bionic/main amd64 libxkbcommon-dev amd64 0.7.1-2 [308 kB] Get:177 http://ftpmaster.internal/ubuntu bionic/main amd64 libmircommon-dev amd64 0.28.1+18.04.20171030-0ubuntu1 [13.9 kB] Get:178 http://ftpmaster.internal/ubuntu bionic/main amd64 libmircookie2 amd64 0.28.1+18.04.20171030-0ubuntu1 [23.4 kB] Get:179 http://ftpmaster.internal/ubuntu bionic/main amd64 libmircookie-dev amd64 0.28.1+18.04.20171030-0ubuntu1 [4404 B] Get:180 http://ftpmaster.internal/ubuntu bionic/main amd64 libmirclient-dev amd64 0.28.1+18.04.20171030-0ubuntu1 [47.8 kB] Get:181 http://ftpmaster.internal/ubuntu bionic/main amd64 libegl1-mesa-dev amd64 17.2.2-0ubuntu1 [19.9 kB] Get:182 http://ftpmaster.internal/ubuntu bionic/main amd64 libgles2-mesa amd64 17.2.2-0ubuntu1 [13.5 kB] Get:183 http://ftpmaster.internal/ubuntu bionic/main amd64 libgles2-mesa-dev amd64 17.2.2-0ubuntu1 [40.3 kB] Get:184 http://ftpmaster.internal/ubuntu bionic/main amd64 libglu1-mesa amd64 9.0.0-2.1build1 [168 kB] Get:185 http://ftpmaster.internal/ubuntu bionic/main amd64 mesa-common-dev amd64 17.2.2-0ubuntu1 [512 kB] Get:186 http://ftpmaster.internal/ubuntu bionic/main amd64 libgl1-mesa-dev amd64 17.2.2-0ubuntu1 [4430 B] Get:187 http://ftpmaster.internal/ubuntu bionic/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1build1 [206 kB] Get:188 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5concurrent5 amd64 5.9.2+dfsg-4ubuntu5 [29.8 kB] Get:189 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5xml5 amd64 5.9.2+dfsg-4ubuntu5 [99.7 kB] Get:190 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5designer5 amd64 5.9.2-3ubuntu1 [2761 kB] Get:191 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5designercomponents5 amd64 5.9.2-3ubuntu1 [692 kB] Get:192 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5sql5 amd64 5.9.2+dfsg-4ubuntu5 [115 kB] Get:193 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5help5 amd64 5.9.2-3ubuntu1 [133 kB] Get:194 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 libqt5quickwidgets5 amd64 5.9.2-3ubuntu1 [35.2 kB] Get:195 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libqt5test5 amd64 5.9.2+dfsg-4ubuntu5 [98.4 kB] Get:196 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 qt5-qmake-bin amd64 5.9.2+dfsg-4ubuntu5 [938 kB] Get:197 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 qtchooser amd64 64-ga1b6736-4 [24.2 kB] Get:198 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 qt5-qmake amd64 5.9.2+dfsg-4ubuntu5 [179 kB] Get:199 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 qtbase5-dev-tools amd64 5.9.2+dfsg-4ubuntu5 [737 kB] Get:200 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 qtbase5-dev amd64 5.9.2+dfsg-4ubuntu5 [942 kB] Get:201 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 qttools5-dev-tools amd64 5.9.2-3ubuntu1 [2138 kB] debconf: delaying package configuration, since apt-utils is not installed 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Setting up libqt5webchannel5:amd64 (5.9.2-2) ... Setting up libxcb-sync-dev:amd64 (1.12-1ubuntu1) ... Setting up fontconfig (2.12.6-0ubuntu1) ... Regenerating fonts cache... done. Setting up libcups2:amd64 (2.2.6-1) ... Setting up libegl1-mesa:amd64 (17.2.2-0ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/mesa-egl/ld.so.conf to provide /etc/ld.so.conf.d/x86_64-linux-gnu_EGL.conf (x86_64-linux-gnu_egl_conf) in auto mode Setting up libx11-xcb-dev:amd64 (2:1.6.4-3) ... Setting up libxcb-render-util0:amd64 (0.3.9-1) ... Setting up libxdamage1:amd64 (1:1.1.4-3) ... Setting up libxcb-image0:amd64 (0.4.0-1build1) ... Setting up mesa-common-dev:amd64 (17.2.2-0ubuntu1) ... Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up x11proto-fixes-dev (1:5.0-2ubuntu2) ... Setting up libmirclient-dev:amd64 (0.28.1+18.04.20171030-0ubuntu1) ... Setting up libxcb-dri2-0-dev:amd64 (1.12-1ubuntu1) ... 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Setting up libxcb-present-dev:amd64 (1.12-1ubuntu1) ... Setting up libqt5quick5:amd64 (5.9.2-3ubuntu1) ... Setting up libqt5widgets5:amd64 (5.9.2+dfsg-4ubuntu5) ... Setting up libqt5printsupport5:amd64 (5.9.2+dfsg-4ubuntu5) ... Setting up libqt5help5:amd64 (5.9.2-3ubuntu1) ... Setting up libgl1-mesa-dev:amd64 (17.2.2-0ubuntu1) ... Setting up libegl1-mesa-dev:amd64 (17.2.2-0ubuntu1) ... Setting up libqt5designer5:amd64 (5.9.2-3ubuntu1) ... Setting up libglu1-mesa-dev:amd64 (9.0.0-2.1build1) ... Setting up libqt5quickwidgets5:amd64 (5.9.2-3ubuntu1) ... Setting up libqt5webkit5:amd64 (5.212.0~alpha2-5) ... Setting up libqt5designercomponents5:amd64 (5.9.2-3ubuntu1) ... Setting up libgles2-mesa-dev:amd64 (17.2.2-0ubuntu1) ... Setting up qttools5-dev-tools (5.9.2-3ubuntu1) ... Setting up qtbase5-dev:amd64 (5.9.2+dfsg-4ubuntu5) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.040-1) ... Setting up debhelper (10.10.5ubuntu1) ... Setting up sbuild-build-depends-clustalx-dummy (0.invalid.0) ... (Reading database ... 21123 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Processing triggers for systemd (235-2ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-97-generic amd64 (x86_64) Toolchain package versions: binutils_2.29.1-6ubuntu1 dpkg-dev_1.19.0.4ubuntu1 g++-7_7.2.0-12ubuntu1 gcc-7_7.2.0-12ubuntu1 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-12ubuntu1 libstdc++6_7.2.0-12ubuntu1 linux-libc-dev_4.13.0-16.19 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.6~alpha3 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu1 autotools-dev_20161112.1+nmu1 base-files_10ubuntu1 base-passwd_3.5.44 bash_4.4-5ubuntu1 binutils_2.29.1-6ubuntu1 binutils-common_2.29.1-6ubuntu1 binutils-x86-64-linux-gnu_2.29.1-6ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu4 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20170717 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Sep 11 12:08:51 2017 UTC gpgv: using RSA key gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./clustalx_2.1+lgpl-6.dsc dpkg-source: info: extracting clustalx in clustalx-2.1+lgpl dpkg-source: info: unpacking clustalx_2.1+lgpl.orig.tar.gz dpkg-source: info: unpacking clustalx_2.1+lgpl-6.debian.tar.xz dpkg-source: info: applying hardcode-accessory-file-locations.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying qt5.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-13653816 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13653816 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13653816 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package clustalx dpkg-buildpackage: info: source version 2.1+lgpl-6 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build clustalx-2.1+lgpl dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory '/<>/clustalx-2.1+lgpl' rm -f moc_* dh_clean make[1]: Leaving directory '/<>/clustalx-2.1+lgpl' debian/rules build dh build dh_update_autotools_config debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/clustalx-2.1+lgpl' qmake Info: creating stash file /<>/clustalx-2.1+lgpl/.qmake.stash # did not found a better way to push hardening flags into Makefile sed -i -e "s:CFLAGS *= .*:& -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security:" \ -e "s:CXXFLAGS *= .*:& -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security:" \ -e "s:LFLAGS *= .*:& -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now:" Makefile make[1]: Leaving directory '/<>/clustalx-2.1+lgpl' dh_auto_build make -j1 make[1]: Entering directory '/<>/clustalx-2.1+lgpl' g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp In file included from clustalW/substitutionMatrix/globalmatrix.h:8:0, from AlignmentParameters.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ AlignmentParameters.cpp: In member function ‘virtual void AlignmentParameters::showEvent(QShowEvent*)’: AlignmentParameters.cpp:48:49: warning: unused parameter ‘event’ [-Wunused-parameter] void AlignmentParameters::showEvent(QShowEvent* event) ^~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68:0: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ AlignmentViewerWidget.cpp: In member function ‘int AlignmentViewerWidget::makeGapPenaltyData()’: AlignmentViewerWidget.cpp:588:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(i = 0; i < len && i < gapMask->size(); i++) ~~^~~~~~~~~~~~~~~~~ AlignmentViewerWidget.cpp: In member function ‘int AlignmentViewerWidget::makeSecStructData()’: AlignmentViewerWidget.cpp:645:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < len && i < _secStructMask->size();i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ AlignmentViewerWidget.cpp:652:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(i = 0; i < len && i < ssMask.size(); i++) ~~^~~~~~~~~~~~~~~ AlignmentViewerWidget.cpp: In member function ‘virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)’: AlignmentViewerWidget.cpp:781:58: warning: unused parameter ‘event’ [-Wunused-parameter] void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) ^~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentWidget.o AlignmentWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, from AlignmentWidget.cpp:49: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from AlignmentWidget.cpp:49:0: AlignmentWidget.h: In constructor ‘AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)’: AlignmentWidget.h:170:10: warning: ‘AlignmentWidget::blackAndWhite’ will be initialized after [-Wreorder] bool blackAndWhite; ^~~~~~~~~~~~~ AlignmentWidget.h:161:27: warning: ‘std::vector >* AlignmentWidget::selectedColoredRes’ [-Wreorder] std::vector* selectedColoredRes; ^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) ^~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function ‘void AlignmentWidget::calculatePixMaps()’: AlignmentWidget.cpp:225:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(unsigned int j = 0; j < lengthLongestSeq; j++) ~~^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:235:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(code >= 0 && code < conservationPixmaps->size()) ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:268:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:280:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:291:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j) ~~~~~~~~~~~~~~~~~~~~~^~~ AlignmentWidget.cpp:215:9: warning: unused variable ‘codeForSpace’ [-Wunused-variable] int codeForSpace = clustalw::userParameters->resIndex( ^~~~~~~~~~~~ AlignmentWidget.cpp: In member function ‘void AlignmentWidget::generateSecStructurePixmaps()’: AlignmentWidget.cpp:333:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i < secStructPixmaps->size() && i < secStructInfo.size()) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function ‘void AlignmentWidget::drawContents(QPainter*, int, int, int, int)’: AlignmentWidget.cpp:569:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(selectedRes >= selectedColoredRes->size()) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function ‘void AlignmentWidget::calcConserveInfo()’: AlignmentWidget.cpp:689:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int j = 1; j <= strongGroup.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:693:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int j = 1; j <= weakGroup.size(); j++) ~~^~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:700:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if((i + _fRes - 1 < (*alignment)[j].size()) && ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:701:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] (i + _fRes - 1 < (*alignment)[_fSeq].size())) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:725:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int k = 1; k <= strongGroup.size(); k++) ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:737:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int k = 1; k <= weakGroup.size(); k++) ~~^~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:760:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int k = 1; k <= strongGroup.size(); k++) ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:771:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int k = 1; k <= weakGroup.size(); k++) ~~^~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function ‘void AlignmentWidget::makeColorMask(clustalw::Array2D*, ColorParameters*)’: AlignmentWidget.cpp:878:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function ‘QString AlignmentWidget::initConsensus()’: AlignmentWidget.cpp:927:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function ‘void AlignmentWidget::generatePixMaps()’: AlignmentWidget.cpp:1039:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int j = 0; j < aminoAcid.size(); j++) ~~^~~~~~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignOutputFileNames.o AlignOutputFileNames.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from AlignOutputFileNames.h:10, from AlignOutputFileNames.cpp:26: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from AlignOutputFileNames.cpp:26:0: AlignOutputFileNames.h:106:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr outFileNames; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from AlignOutputFileNames.h:9, from AlignOutputFileNames.cpp:26: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from BootstrapTreeDialog.h:11, from BootstrapTreeDialog.cpp:18: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from BootstrapTreeDialog.cpp:18:0: BootstrapTreeDialog.h:70:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from BootstrapTreeDialog.h:10, from BootstrapTreeDialog.cpp:18: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColorFileXmlParser.o ColorFileXmlParser.cpp ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] // tr("colorrules not found in the parameter file, using\ ^ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from ColorFileXmlParser.h:9, from ColorFileXmlParser.cpp:3: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ColorFileXmlParser.cpp: In member function ‘int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)’: ColorFileXmlParser.cpp:85:46: warning: unused parameter ‘parentItem’ [-Wunused-parameter] QTreeWidgetItem *parentItem) ^~~~~~~~~~ ColorFileXmlParser.cpp: In member function ‘void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)’: ColorFileXmlParser.cpp:138:86: warning: unused parameter ‘parentItem’ [-Wunused-parameter] void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) ^~~~~~~~~~ ColorFileXmlParser.cpp: In member function ‘int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)’: ColorFileXmlParser.cpp:175:85: warning: unused parameter ‘parentItem’ [-Wunused-parameter] int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) ^~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from ColorParameters.cpp:1: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ColorParameters.cpp: In member function ‘QColor ColorParameters::getResidueColor(QChar, QChar)’: ColorParameters.cpp:160:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(i = 0; i < colorPar.size(); i++) ~~^~~~~~~~~~~~~~~~~ ColorParameters.cpp:174:26: warning: unused variable ‘temp’ [-Wunused-variable] char temp = colorPar[i].consensusConditionList[j].toLatin1(); ^~~~ ColorParameters.cpp:157:10: warning: unused variable ‘showRes’ [-Wunused-variable] char showRes = res.toLatin1(); ^~~~~~~ ColorParameters.cpp:158:10: warning: unused variable ‘showCon’ [-Wunused-variable] char showCon = consensus.toLatin1(); ^~~~~~~ ColorParameters.cpp: In member function ‘int ColorParameters::getResidueColorNum(QChar, QChar)’: ColorParameters.cpp:197:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(i = 0; i < colorPar.size(); i++) ~~^~~~~~~~~~~~~~~~~ ColorParameters.cpp:211:26: warning: unused variable ‘temp’ [-Wunused-variable] char temp = colorPar[i].consensusConditionList[j].toLatin1(); ^~~~ ColorParameters.cpp:194:10: warning: unused variable ‘showRes’ [-Wunused-variable] char showRes = res.toLatin1(); ^~~~~~~ ColorParameters.cpp:195:10: warning: unused variable ‘showCon’ [-Wunused-variable] char showCon = consensus.toLatin1(); ^~~~~~~ ColorParameters.cpp: In member function ‘void ColorParameters::printColorInfo()’: ColorParameters.cpp:229:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 0; i < colors.size(); i++) ~~^~~~~~~~~~~~~~~ ColorParameters.cpp: In member function ‘int ColorParameters::getIndexOfColor(QColor)’: ColorParameters.cpp:238:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 0; i < colors.size(); i++) ~~^~~~~~~~~~~~~~~ ColorParameters.cpp: In member function ‘QColor ColorParameters::getColorFromNum(int)’: ColorParameters.cpp:251:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(colorNum > 0 && colorNum - 1 < colorPar.size()) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp In file included from clustalW/substitutionMatrix/globalmatrix.h:8:0, from ColumnScoreParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ColumnScoreParams.cpp: In member function ‘virtual void ColumnScoreParams::showEvent(QShowEvent*)’: ColumnScoreParams.cpp:51:47: warning: unused parameter ‘event’ [-Wunused-parameter] void ColumnScoreParams::showEvent(QShowEvent* event) ^~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from HardCodedColorScheme.cpp:1: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HelpDisplayWidget.h:18, from HelpDisplayWidget.cpp:15: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ HelpDisplayWidget.cpp: In member function ‘std::__cxx11::string* HelpDisplayWidget::loadHelpInformation(char)’: HelpDisplayWidget.cpp:61:13: warning: variable ‘number’ set but not used [-Wunused-but-set-variable] int i, number, nlines; ^~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp HistogramWidget.cpp: In member function ‘void HistogramWidget::drawContents(QPainter*, int, int, int, int)’: HistogramWidget.cpp:180:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(column >= 0 && column < arrayOfHeights->size()) ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ HistogramWidget.cpp:198:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(column >= 0 && column < arrayOfHeights->size()) ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp In file included from clustalW/substitutionMatrix/globalmatrix.h:8:0, from LowScoringSegParams.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ LowScoringSegParams.cpp: In member function ‘virtual void LowScoringSegParams::showEvent(QShowEvent*)’: LowScoringSegParams.cpp:51:49: warning: unused parameter ‘event’ [-Wunused-parameter] void LowScoringSegParams::showEvent(QShowEvent* event) ^~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp In file included from main.cpp:21:0: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/Clustal.h:18:0, from mainwindow.h:45, from main.cpp:24: clustalW/fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from main.cpp:24: clustalW/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 clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/Clustal.h:18:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mainwindow.cpp:99:0: WritePostscriptFile.h:88:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr params; ^~~~~~~~ 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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mainwindow.cpp:100:0: AlignOutputFileNames.h:106:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr outFileNames; ^~~~~~~~ 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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mainwindow.cpp:101:0: TreeOutputFileNames.h:73:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ 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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mainwindow.cpp:102:0: BootstrapTreeDialog.h:70:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ 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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ mainwindow.cpp: In member function ‘virtual void MainWindow::showEvent(QShowEvent*)’: mainwindow.cpp:198:40: warning: unused parameter ‘event’ [-Wunused-parameter] void MainWindow::showEvent(QShowEvent* event) ^~~~~ mainwindow.cpp: In member function ‘void MainWindow::writeViewer1AsPostscript(int)’: mainwindow.cpp:1454:47: warning: unused parameter ‘type’ [-Wunused-parameter] void MainWindow::writeViewer1AsPostscript(int type) ^~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp In file included from clustalW/substitutionMatrix/globalmatrix.h:8:0, from PairwiseParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ PairwiseParams.cpp: In member function ‘virtual void PairwiseParams::showEvent(QShowEvent*)’: PairwiseParams.cpp:74:44: warning: unused parameter ‘event’ [-Wunused-parameter] void PairwiseParams::showEvent(QShowEvent* event) ^~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from PostscriptFileParams.h:4, from PostscriptFileParams.cpp:1: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from PSPrinter.h:11, from PSPrinter.cpp:20: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ PSPrinter.cpp: In member function ‘void PSPrinter::writePSFile(PostscriptFileParams*)’: PSPrinter.cpp:207:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res.isLetter() && resNumber.size() > i - data->firstSeq) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ PSPrinter.cpp:307:67: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res.isLetter() && resNumber.size() > seq) ~~~~~~~~~~~~~~~~~^~~~~ PSPrinter.cpp:421:67: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res.isLetter() && resNumber.size() > i) ~~~~~~~~~~~~~~~~~^~~ PSPrinter.cpp:55:9: warning: unused variable ‘err’ [-Wunused-variable] int err; ^~~ PSPrinter.cpp:73:9: warning: unused variable ‘gapPos1’ [-Wunused-variable] int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local ^~~~~~~ PSPrinter.cpp:74:9: warning: unused variable ‘gapPos2’ [-Wunused-variable] int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local ^~~~~~~ PSPrinter.cpp: In member function ‘void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)’: PSPrinter.cpp:587:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(data->nameHeader.size() > ix) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ PSPrinter.cpp: In member function ‘void PSPrinter::printFooterLine(std::ofstream*, int, int)’: PSPrinter.cpp:730:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(i = fr; i <= lr && i < ruler.length(); i++) ~~^~~~~~~~~~~~~~~~ PSPrinter.cpp: In member function ‘void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)’: PSPrinter.cpp:789:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~ PSPrinter.cpp:781:14: warning: unused variable ‘psY’ [-Wunused-variable] int psX, psY, curveBottom; ^~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26:0: clustalW/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 clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from SeqNameWidget.cpp:59: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/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"); ^~~~~~~~~~~~~~ SeqNameWidget.cpp: In member function ‘virtual void SeqNameWidget::paintEvent(QPaintEvent*)’: SeqNameWidget.cpp:375:11: warning: variable ‘redrawRect’ set but not used [-Wunused-but-set-variable] QRect redrawRect = event->rect(); ^~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from TreeOutputFileNames.h:10, from TreeOutputFileNames.cpp:17: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from TreeOutputFileNames.cpp:17:0: TreeOutputFileNames.h:73:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from TreeOutputFileNames.h:9, from TreeOutputFileNames.cpp:17: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from WritePostscriptFile.h:10, from WritePostscriptFile.cpp:24: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from WritePostscriptFile.cpp:24:0: WritePostscriptFile.h:88:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr params; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27:0: clustalW/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 WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/fileInput/../alignment/Alignment.h:42, from clustalW/fileInput/FileReader.h:12, from clustalW/Clustal.h:18, from clustalW/Clustal.cpp:27: clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/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 clustalW/Clustal.h:18:0, from clustalW/Clustal.cpp:27: clustalW/fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:68:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ 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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from clustalW/Clustal.cpp:27: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33:0: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33:0: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33:0: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33:0: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33:0: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33:0: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33:0: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/Clustal.cpp: In member function ‘void clustalw::Clustal::align(std::__cxx11::string*, bool)’: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/Clustal.cpp: In member function ‘void clustalw::Clustal::doAlignUseOldTree(std::__cxx11::string*)’: clustalW/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 clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from clustalW/alignment/Alignment.cpp:25: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/Alignment.cpp: In member function ‘bool clustalw::Alignment::keepPortionOfSeqArray(int, int)’: clustalW/alignment/Alignment.cpp:1715:24: warning: variable ‘posToAddTo’ set but not used [-Wunused-but-set-variable] SeqArray::iterator posToAddTo = sectionToRealign.begin(); ^~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from clustalW/alignment/AlignmentOutput.h:24, from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/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 clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/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 clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/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 clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/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 clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/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 clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/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 clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/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 clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/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 clustalW/alignment/AlignmentOutput.cpp:27:0: clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/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 clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/ObjectiveScore.h:15, from clustalW/alignment/ObjectiveScore.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/fileInput/../alignment/Alignment.h:42, from clustalW/fileInput/FileReader.h:12, from clustalW/fileInput/FileReader.cpp:29: clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/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 clustalW/fileInput/FileReader.cpp:29:0: clustalW/fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/fileInput/FileReader.h:11, from clustalW/fileInput/FileReader.cpp:29: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/fileInput/FileReader.cpp: In member function ‘int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::__cxx11::string*)’: clustalW/fileInput/FileReader.cpp:155:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fileParser; // Means we dont need to delete it! ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/fileInput/FileReader.h:11, from clustalW/fileInput/FileReader.cpp:29: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/fileInput/FileReader.cpp: At global scope: clustalW/fileInput/FileReader.cpp:426:42: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/fileInput/FileReader.h:11, from clustalW/fileInput/FileReader.cpp:29: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp clustalW/fileInput/MSFFileParser.cpp: In member function ‘virtual std::vector clustalw::MSFFileParser::getSeqRange(int, int, std::__cxx11::string*)’: clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter ‘offendingSeq’ [-Wunused-parameter] vector MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) ^~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp: In member function ‘virtual void clustalw::MSFFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)’: clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter ‘gapPenaltyMask’ [-Wunused-parameter] void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ^~~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter ‘secStructMask’ [-Wunused-parameter] void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ^~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter ‘secStructName’ [-Wunused-parameter] string& secStructName, int &structPenalties, int length) ^~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter ‘length’ [-Wunused-parameter] string& secStructName, int &structPenalties, int length) ^~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp clustalW/fileInput/PearsonFileParser.cpp: In member function ‘virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::__cxx11::string*)’: clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter ‘offendingSeq’ [-Wunused-parameter] Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) ^~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp: In member function ‘virtual void clustalw::PearsonFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)’: clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter ‘gapPenaltyMask’ [-Wunused-parameter] void PearsonFileParser::getSecStructure(vector& gapPenaltyMask, ^~~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter ‘secStructMask’ [-Wunused-parameter] vector& secStructMask, string& secStructName, ^~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter ‘secStructName’ [-Wunused-parameter] vector& secStructMask, string& secStructName, ^~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter ‘length’ [-Wunused-parameter] int &structPenalties, int length) ^~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp clustalW/fileInput/PIRFileParser.cpp: In member function ‘virtual void clustalw::PIRFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)’: clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter ‘gapPenaltyMask’ [-Wunused-parameter] void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ^~~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:292:81: warning: unused parameter ‘secStructMask’ [-Wunused-parameter] void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ^~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:293:45: warning: unused parameter ‘secStructName’ [-Wunused-parameter] string& secStructName, int &structPenalties, int length) ^~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter ‘length’ [-Wunused-parameter] string& secStructName, int &structPenalties, int length) ^~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp clustalW/fileInput/RSFFileParser.cpp: In member function ‘virtual void clustalw::RSFFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)’: clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter ‘gapPenaltyMask’ [-Wunused-parameter] void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp clustalW/general/ClustalWResources.cpp: In member function ‘std::__cxx11::string clustalw::ClustalWResources::findFile(std::__cxx11::string, clustalw::ClustalWResourcePathType) const’: clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript is above array bounds [-Warray-bounds] delim[1] = 0; ~~~~~~~^ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp In file included from clustalW/general/OutputFile.cpp:9:0: clustalW/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 clustalW/general/OutputFile.h:8, from clustalW/general/OutputFile.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/general/../alignment/Alignment.h:42, from clustalW/general/Stats.cpp:15: clustalW/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"); ^~~~~~~~~~~~~~ clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp clustalW/general/UserParameters.cpp: In constructor ‘clustalw::UserParameters::UserParameters(bool)’: clustalW/general/UserParameters.cpp:33:37: warning: unused parameter ‘log’ [-Wunused-parameter] UserParameters::UserParameters(bool log) ^~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp clustalW/general/Utility.cpp: In member function ‘bool clustalw::Utility::lineType(char*, const char*)’: clustalW/general/Utility.cpp:251:8: warning: variable ‘n’ set but not used [-Wunused-but-set-variable] int n; ^ clustalW/general/Utility.cpp: In member function ‘virtual void clustalw::Utility::setInfoLabelPtr(QLabel*)’: clustalW/general/Utility.cpp:519:39: warning: unused parameter ‘ptrToLabelObj’ [-Wunused-parameter] void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) ^~~~~~~~~~~~~ clustalW/general/Utility.cpp: In member function ‘double clustalw::Utility::getReal(const char*, double, double, double)’: clustalW/general/Utility.cpp:183:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ clustalW/general/Utility.cpp: In member function ‘int clustalw::Utility::getInt(const char*, int, int, int)’: clustalW/general/Utility.cpp:221:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/interface/../fileInput/../alignment/Alignment.h:42, from clustalW/interface/../fileInput/FileReader.h:12, from clustalW/interface/../Clustal.h:18, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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"); ^~~~~~~~~~~~~~ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/interface/../Clustal.h:18:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/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 clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/interface/../fileInput/../alignment/Alignment.h:42, from clustalW/interface/../fileInput/FileReader.h:12, from clustalW/interface/../Clustal.h:18, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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"); ^~~~~~~~~~~~~~ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/interface/../Clustal.h:18:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/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 clustalW/interface/../Clustal.h:20:0, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/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 clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/interface/InteractiveMenu.cpp: In member function ‘int clustalw::InteractiveMenu::secStrOutputOptions()’: clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] clustalObj->getHelp('C'); ~~~~~~~~~~~~~~~~~~~^~~~~ clustalW/interface/InteractiveMenu.cpp:521:13: note: here case 'Q': ^~~~ clustalW/interface/InteractiveMenu.cpp: In member function ‘void clustalw::InteractiveMenu::doSystem()’: clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(lin1.c_str()); ~~~~~~^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17:0: clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/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 clustalW/multipleAlign/Iteration.cpp:17:0: clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/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 clustalW/multipleAlign/Iteration.cpp:17:0: clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/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 clustalW/multipleAlign/Iteration.cpp:17:0: clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/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 clustalW/multipleAlign/Iteration.cpp:17:0: clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/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 clustalW/multipleAlign/Iteration.cpp:17:0: clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/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 clustalW/multipleAlign/Iteration.cpp:17:0: clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/multipleAlign/Iteration.cpp: In member function ‘bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)’: clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] int count; ^~~~~ clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] tmpnam (buffer); ~~~~~~~^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/LowScoreSegProfile.h:13, from clustalW/multipleAlign/LowScoreSegProfile.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, from clustalW/multipleAlign/MSA.h:10, from clustalW/multipleAlign/MSA.cpp:16: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/MSA.cpp: In member function ‘int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, clustalw::AlignmentSteps*, int)’: clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable ‘alignmentScore’ [-Wunused-variable] int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 ^~~~~~~~~~~~~~ clustalW/multipleAlign/MSA.cpp: In member function ‘int clustalw::MSA::seqsAlignToProfile(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, int, std::__cxx11::string)’: clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter ‘phylipName’ [-Wunused-parameter] string phylipName) ^~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, from clustalW/multipleAlign/MyersMillerProfileAlign.h:10, from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, from clustalW/multipleAlign/ProfileBase.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileStandard.h:9, from clustalW/multipleAlign/ProfileStandard.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileWithSub.h:9, from clustalW/multipleAlign/ProfileWithSub.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, from clustalW/pairwise/FastPairwiseAlign.h:9, from clustalW/pairwise/FastPairwiseAlign.cpp:10: clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, from clustalW/pairwise/FullPairwiseAlign.h:9, from clustalW/pairwise/FullPairwiseAlign.cpp:9: clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15:0: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function ‘void clustalw::SubMatrix::tempInterface(int, int)’: clustalW/substitutionMatrix/SubMatrix.cpp:1613:35: warning: unused parameter ‘alignResidueType’ [-Wunused-parameter] void SubMatrix::tempInterface(int alignResidueType, int alignType) ^~~~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp:1613:57: warning: unused parameter ‘alignType’ [-Wunused-parameter] void SubMatrix::tempInterface(int alignResidueType, int alignType) ^~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function ‘void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])’: clustalW/substitutionMatrix/SubMatrix.cpp:1657:9: warning: variable ‘maxRes’ set but not used [-Wunused-but-set-variable] int maxRes; ^~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function ‘void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])’: clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable ‘maxRes’ set but not used [-Wunused-but-set-variable] int maxRes; ^~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function ‘int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)’: clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: ‘n’ may be used uninitialized in this function [-Wmaybe-uninitialized] return (maxRes); ^ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTree.h:20, from clustalW/tree/ClusterTree.cpp:9: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23:0, from clustalW/tree/ClusterTree.cpp:9: clustalW/tree/../general/OutputFile.h:26:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/tree/ClusterTree.h:16, from clustalW/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 clustalW/tree/ClusterTree.cpp:9:0: clustalW/tree/ClusterTree.h:70:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/tree/ClusterTree.h:16, from clustalW/tree/ClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/ClusterTree.cpp: In member function ‘void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)’: clustalW/tree/ClusterTree.cpp:580:9: warning: variable ‘rs’ set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^~ clustalW/tree/ClusterTree.cpp:580:17: warning: variable ‘rl’ set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTreeOutput.h:11, from clustalW/tree/ClusterTreeOutput.cpp:9: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/../alignment/../general/clustalw.h:44:0, from clustalW/tree/../alignment/../general/Utility.h:15, from clustalW/tree/../alignment/../general/utils.h:8, from clustalW/tree/../alignment/../general/UserParameters.h:22, from clustalW/tree/../alignment/../general/userparams.h:8, from clustalW/tree/../alignment/Sequence.h:20, from clustalW/tree/../alignment/Alignment.h:41, from clustalW/tree/ClusterTreeOutput.h:11, from clustalW/tree/ClusterTreeOutput.cpp:9: clustalW/tree/../alignment/../general/SymMatrix.h: In member function ‘void clustalw::ClusterTreeOutput::printPhylipTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector*)’: clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ clustalW/tree/../alignment/../general/SymMatrix.h: In member function ‘void clustalw::ClusterTreeOutput::printNexusTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector*)’: clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp In file included from clustalW/tree/../general/clustalw.h:44:0, from clustalW/tree/ClusterTreeAlgorithm.h:12, from clustalW/tree/NJTree.h:11, from clustalW/tree/NJTree.cpp:10: clustalW/tree/../general/SymMatrix.h: In member function ‘virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)’: clustalW/tree/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ clustalW/tree/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/Tree.h:13, from clustalW/tree/Tree.cpp:10: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/Tree.cpp:10:0: clustalW/tree/Tree.h:26:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr createSets(int firstSeq, int lastSeq); ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/tree/../alignment/Alignment.h:38, from clustalW/tree/Tree.h:13, from clustalW/tree/Tree.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/Tree.cpp:278:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr Tree::createSets(int firstSeq, int lastSeq) ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/tree/../alignment/Alignment.h:38, from clustalW/tree/Tree.h:13, from clustalW/tree/Tree.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/Tree.cpp: In member function ‘std::auto_ptr clustalw::Tree::createSets(int, int)’: clustalW/tree/Tree.cpp:280:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr progAlignSteps; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/tree/../alignment/Alignment.h:38, from clustalW/tree/Tree.h:13, from clustalW/tree/Tree.cpp:10: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/TreeInterface.h:19, from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:15:0: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/TreeInterface.cpp:15:0: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/TreeInterface.cpp:15:0: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/TreeInterface.cpp:15:0: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/TreeInterface.cpp:15:0: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/TreeInterface.cpp:15:0: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/TreeInterface.cpp:15:0: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/ClusterTree.h:23:0, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/TreeInterface.cpp:17: clustalW/tree/../general/OutputFile.h:26:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/UnRootedClusterTree.h:8:0, from clustalW/tree/TreeInterface.cpp:17: clustalW/tree/ClusterTree.h:70:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/TreeInterface.cpp:18:0: clustalW/tree/Tree.h:26:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr createSets(int firstSeq, int lastSeq); ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/tree/TreeInterface.h:17, from clustalW/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 clustalW/tree/TreeInterface.cpp:23:0: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp:195:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)’: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: At global scope: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::__cxx11::string*, std::vector*, int, int, bool*)’: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: At global scope: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::__cxx11::string*, std::vector*, int, int, bool*)’: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: At global scope: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)’: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: At global scope: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)’: clustalW/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 clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTree.h:20, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23:0, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: clustalW/tree/../general/OutputFile.h:26:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/tree/ClusterTree.h:16, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/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 clustalW/tree/UnRootedClusterTree.h:8:0, from clustalW/tree/UnRootedClusterTree.cpp:9: clustalW/tree/ClusterTree.h:70:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from clustalW/tree/ClusterTree.h:16, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/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 clustalW/tree/../alignment/../general/clustalw.h:44:0, from clustalW/tree/../alignment/../general/Utility.h:15, from clustalW/tree/../alignment/../general/utils.h:8, from clustalW/tree/../alignment/../general/UserParameters.h:22, from clustalW/tree/../alignment/../general/userparams.h:8, from clustalW/tree/../alignment/Sequence.h:20, from clustalW/tree/../alignment/Alignment.h:41, from clustalW/tree/ClusterTree.h:20, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: clustalW/tree/../alignment/../general/SymMatrix.h: In member function ‘void clustalw::UnRootedClusterTree::treeFromDistMatrix(clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string&)’: clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/../ClusterTree.h:20, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/UPGMA/../ClusterTree.h:23:0, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/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 clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/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 clustalW/tree/UPGMA/RootedClusterTree.h:8:0, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/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 clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/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 clustalW/tree/UPGMA/RootedClusterTree.cpp:9:0: clustalW/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 clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/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 clustalW/tree/UPGMA/RootedClusterTree.cpp:11:0: clustalW/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 clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/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 clustalW/tree/UPGMA/RootedClusterTree.cpp:11:0: clustalW/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 clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/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 clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/UPGMA/RootedClusterTree.cpp: In member function ‘std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string&)’: clustalW/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 clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/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 clustalW/tree/UPGMA/../../alignment/../general/clustalw.h:44:0, from clustalW/tree/UPGMA/../../alignment/../general/Utility.h:15, from clustalW/tree/UPGMA/../../alignment/../general/utils.h:8, from clustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22, from clustalW/tree/UPGMA/../../alignment/../general/userparams.h:8, from clustalW/tree/UPGMA/../../alignment/Sequence.h:20, from clustalW/tree/UPGMA/../../alignment/Alignment.h:41, from clustalW/tree/UPGMA/../ClusterTree.h:20, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, from clustalW/tree/UPGMA/RootedGuideTree.cpp:10: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, from clustalW/tree/UPGMA/RootedTreeOutput.h:15, from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/UPGMA/../../alignment/../general/clustalw.h:44:0, from clustalW/tree/UPGMA/../../alignment/../general/Utility.h:15, from clustalW/tree/UPGMA/../../alignment/../general/utils.h:8, from clustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22, from clustalW/tree/UPGMA/../../alignment/../general/userparams.h:8, from clustalW/tree/UPGMA/../../alignment/Sequence.h:20, from clustalW/tree/UPGMA/../../alignment/Alignment.h:41, from clustalW/tree/UPGMA/RootedGuideTree.h:17, from clustalW/tree/UPGMA/RootedTreeOutput.h:15, from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function ‘void clustalw::RootedTreeOutput::printPhylipTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)’: clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function ‘void clustalw::RootedTreeOutput::printNexusTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)’: clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^~ g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:8, from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:0: clustalW/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 clustalW/tree/UPGMA/../../general/SquareMat.h:9, from clustalW/tree/UPGMA/../../general/clustalw.h:43, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6, from clustalW/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 clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:0: clustalW/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 clustalW/tree/UPGMA/../../general/SquareMat.h:9, from clustalW/tree/UPGMA/../../general/clustalw.h:43, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6, from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/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 clustalW/tree/UPGMA/../../general/SquareMat.h:9, from clustalW/tree/UPGMA/../../general/clustalw.h:43, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6, from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -pipe -O2 -Wall -W -dM -E -o moc_predefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/features/data/dummy.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from moc_AlignmentViewerWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, from moc_AlignmentWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from AlignOutputFileNames.h:10, from moc_AlignOutputFileNames.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from moc_AlignOutputFileNames.cpp:9:0: AlignOutputFileNames.h:106:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr outFileNames; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from AlignOutputFileNames.h:9, from moc_AlignOutputFileNames.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from BootstrapTreeDialog.h:11, from moc_BootstrapTreeDialog.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from moc_BootstrapTreeDialog.cpp:9:0: BootstrapTreeDialog.h:70:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from BootstrapTreeDialog.h:10, from moc_BootstrapTreeDialog.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from ColorFileXmlParser.h:9, from moc_ColorFileXmlParser.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include ColumnScoreParams.h -o moc_ColumnScoreParams.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include FileDialog.h -o moc_FileDialog.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HelpDisplayWidget.h:18, from moc_HelpDisplayWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include HistogramWidget.h -o moc_HistogramWidget.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include LowScoringSegParams.h -o moc_LowScoringSegParams.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include mainwindow.h -o moc_mainwindow.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/Clustal.h:18:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20:0, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/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 clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include ProteinGapParameters.h -o moc_ProteinGapParameters.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include PSPrinter.h -o moc_PSPrinter.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from PSPrinter.h:11, from moc_PSPrinter.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from moc_SaveSeqFile.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include SearchForString.h -o moc_SearchForString.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include SecStructOptions.h -o moc_SecStructOptions.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include SeqNameWidget.h -o moc_SeqNameWidget.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from moc_SeqNameWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include TreeFormatOptions.h -o moc_TreeFormatOptions.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from TreeOutputFileNames.h:10, from moc_TreeOutputFileNames.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from moc_TreeOutputFileNames.cpp:9:0: TreeOutputFileNames.h:73:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from TreeOutputFileNames.h:9, from moc_TreeOutputFileNames.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include ./moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl -I/<>/clustalx-2.1+lgpl/clustalW/general -I/<>/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/<>/clustalx-2.1+lgpl/clustalW/alignment -I/<>/clustalx-2.1+lgpl/clustalW -I/<>/clustalx-2.1+lgpl/clustalW/fileInput -I/<>/clustalx-2.1+lgpl/clustalW/interface -I/<>/clustalx-2.1+lgpl/clustalW/pairwise -I/<>/clustalx-2.1+lgpl/clustalW/multipleAlign -I/<>/clustalx-2.1+lgpl/clustalW/tree -I/<>/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include WritePostscriptFile.h -o moc_WritePostscriptFile.cpp g++ -c -pipe -O2 -Wall -W -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -fdebug-prefix-map=/<>/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from WritePostscriptFile.h:10, from moc_WritePostscriptFile.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from moc_WritePostscriptFile.cpp:9:0: WritePostscriptFile.h:88:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr params; ^~~~~~~~ In file included from /usr/include/c++/7/memory:80:0, from WritePostscriptFile.h:9, from moc_WritePostscriptFile.cpp:9: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o -lQt5Widgets -lQt5Gui -lQt5Xml -lQt5Core -lGL -lpthread Iteration.o: In function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./clustalW/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[1]: Leaving directory '/<>/clustalx-2.1+lgpl' dh_auto_test fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/clustalx-2.1+lgpl' dh_installchangelogs debian/CHANGELOG.upstream make[1]: Leaving directory '/<>/clustalx-2.1+lgpl' dh_installman dh_installmime dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing clustalx (in debian/clustalx); do_strip: , oemstrip: pkgstriptranslations: processing clustalx-dbgsym (in debian/.debhelper/clustalx/dbgsym-root); do_strip: , oemstrip: debian/clustalx/usr/share/applications/clustalx.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/clustalx/DEBIAN/control, package clustalx, directory debian/clustalx .. removing usr/share/doc/clustalx/changelog.gz pkgstripfiles: Truncating usr/share/doc/clustalx/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package clustalx ... pkgstripfiles: No PNG files. dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-6_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/clustalx/dbgsym-root/DEBIAN/control, package clustalx-dbgsym, directory debian/.debhelper/clustalx/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package clustalx-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'clustalx-dbgsym' in 'debian/.debhelper/scratch-space/build-clustalx/clustalx-dbgsym_2.1+lgpl-6_amd64.deb'. Renaming clustalx-dbgsym_2.1+lgpl-6_amd64.deb to clustalx-dbgsym_2.1+lgpl-6_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../clustalx_2.1+lgpl-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build clustalx-2.1+lgpl dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171103-1136 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ clustalx_2.1+lgpl-6_amd64.changes: ---------------------------------- Format: 1.8 Date: Mon, 11 Sep 2017 14:03:26 +0200 Source: clustalx Binary: clustalx Architecture: amd64 Version: 2.1+lgpl-6 Distribution: bionic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: clustalx - Multiple alignment of nucleic acid and protein sequences (graphic Closes: 874851 Changes: clustalx (2.1+lgpl-6) unstable; urgency=medium . [ Andreas Tille ] * cme fix dpkg-copyright * port to Qt5 Closes: #874851 * debian/clustalx.desktop: Add %f to Exec field * Standards-Version: 4.1.0 (no changes needed) . [ Steffen Moeller ] * debian/upstream/metadata: - added references to registries - yamllint cleanliness Checksums-Sha1: f64907e4bfd210f38bd58848c1c8235127c14fd8 10105488 clustalx-dbgsym_2.1+lgpl-6_amd64.ddeb aca1c4600fb4095fefaafd761dc32ace126e8375 11345 clustalx_2.1+lgpl-6_amd64.buildinfo 01d743dd1eea97efd9d48e449578330d66a2f2fa 435188 clustalx_2.1+lgpl-6_amd64.deb Checksums-Sha256: 550a18ad7c26e6ab63f27437aed210b9b45604fe452e40b95b18f9cb0e604be7 10105488 clustalx-dbgsym_2.1+lgpl-6_amd64.ddeb f6a3748b2cb938f1efb80f9d2b5ddce8ae721ad367c780ece6fb8d0c229b63cb 11345 clustalx_2.1+lgpl-6_amd64.buildinfo 79e6ef94dd72409b2d3eee7c8f0070c9cfaeb0987fc4bba1a73bc106e535c833 435188 clustalx_2.1+lgpl-6_amd64.deb Files: abc0ef3c1a6c248f6b656846734040d8 10105488 debug optional clustalx-dbgsym_2.1+lgpl-6_amd64.ddeb 947ed67c4038fc5cbd39168ca68bd141 11345 science optional clustalx_2.1+lgpl-6_amd64.buildinfo 05b466b477ea43548d542eefacb34b9a 435188 science optional clustalx_2.1+lgpl-6_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ clustalx_2.1+lgpl-6_amd64.deb ----------------------------- new debian package, version 2.0. size 435188 bytes: control archive=1468 bytes. 1603 bytes, 28 lines control 804 bytes, 12 lines md5sums Package: clustalx Version: 2.1+lgpl-6 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1350 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libqt5core5a (>= 5.9.0~beta), libqt5gui5 (>= 5.2.0), libqt5widgets5 (>= 5.0.2), libqt5xml5 (>= 5.0.2), libstdc++6 (>= 5.2) Suggests: clustalw, texlive-latex-extra, boxshade Section: science Priority: optional Homepage: http://www.clustal.org/clustal2/ Description: Multiple alignment of nucleic acid and protein sequences (graphical interface) This package offers a GUI interface for the Clustal multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated to highlight conserved features in the alignment. For professional presentations, one should use the texshade LaTeX package or boxshade. . The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment. . An alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. drwxr-xr-x root/root 0 2017-09-11 12:03 ./ drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/ drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/bin/ -rwxr-xr-x root/root 1271112 2017-09-11 12:03 ./usr/bin/clustalx drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/lib/ drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/lib/mime/ drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/lib/mime/packages/ -rw-r--r-- root/root 114 2017-09-11 12:03 ./usr/lib/mime/packages/clustalx drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/ drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/applications/ -rw-r--r-- root/root 876 2017-09-11 12:03 ./usr/share/applications/clustalx.desktop drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/clustalx/ -rw-r--r-- root/root 69428 2010-11-17 10:12 ./usr/share/clustalx/clustalx.hlp -rw-r--r-- root/root 847 2010-11-17 10:12 ./usr/share/clustalx/coldna.xml -rw-r--r-- root/root 1276 2010-11-17 10:12 ./usr/share/clustalx/colprint.xml -rw-r--r-- root/root 5047 2010-11-17 10:12 ./usr/share/clustalx/colprot.xml drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/doc/clustalx/ -rw-r--r-- root/root 410 2017-09-11 12:03 ./usr/share/doc/clustalx/README.Debian -rw-r--r-- root/root 1938 2017-09-11 12:03 ./usr/share/doc/clustalx/changelog.Debian.gz -rw-r--r-- root/root 1826 2017-09-11 12:03 ./usr/share/doc/clustalx/copyright drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/man/ drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/man/man1/ -rw-r--r-- root/root 797 2017-09-11 12:03 ./usr/share/man/man1/clustalx.1.gz drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/mime/ drwxr-xr-x root/root 0 2017-09-11 12:03 ./usr/share/mime/packages/ -rw-r--r-- root/root 513 2017-09-11 12:03 ./usr/share/mime/packages/clustalx.xml +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 138100 Build-Time: 500 Distribution: bionic-proposed Host Architecture: amd64 Install-Time: 68 Job: clustalx_2.1+lgpl-6.dsc Machine Architecture: amd64 Package: clustalx Package-Time: 571 Source-Version: 2.1+lgpl-6 Space: 138100 Status: successful Version: 2.1+lgpl-6 -------------------------------------------------------------------------------- Finished at 20171103-1136 Build needed 00:09:31, 138100k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13653816 Scanning for processes to kill in build PACKAGEBUILD-13653816 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13653816 Stopping target for build PACKAGEBUILD-13653816 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13653816 Removing build PACKAGEBUILD-13653816