I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 18 23:21:08 +14 2023 I: pbuilder-time-stamp: 1681809668 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [clustalx_2.1+lgpl-9.dsc] I: copying [./clustalx_2.1+lgpl.orig.tar.gz] I: copying [./clustalx_2.1+lgpl-9.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Dec 5 12:20:42 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./clustalx_2.1+lgpl-9.dsc: no acceptable signature found 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-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardcode-accessory-file-locations.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying qt5.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/303538/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 18 23:21 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/303538/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/303538/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6e57f76f40e74c3cbe8a1b65e4510b06 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=303538 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.K8kXgF8Q/pbuilderrc_n0rb --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.K8kXgF8Q/b2 --logfile b2/build.log --extrapackages usrmerge clustalx_2.1+lgpl-9.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Apr 18 23:21 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/303538/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), qtbase5-dev, qtbase5-dev-tools, qttools5-dev-tools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on qtbase5-dev; however: Package qtbase5-dev is not installed. pbuilder-satisfydepends-dummy depends on qtbase5-dev-tools; however: Package qtbase5-dev-tools is not installed. pbuilder-satisfydepends-dummy depends on qttools5-dev-tools; however: Package qttools5-dev-tools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} iso-codes{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libbsd0{a} libcap2-bin{a} libclang1-14{a} libcups2{a} libdbus-1-3{a} libdebhelper-perl{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdw1{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libelf1{a} libevdev2{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgbm1{a} libgl-dev{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgstreamer-plugins-base1.0-0{a} libgstreamer1.0-0{a} libgudev-1.0-0{a} libharfbuzz0b{a} libhyphen0{a} libice6{a} libicu72{a} libinput-bin{a} libinput10{a} libjpeg62-turbo{a} libllvm14{a} libllvm15{a} libmagic-mgc{a} libmagic1{a} libmd4c0{a} libmtdev1{a} libopengl-dev{a} libopengl0{a} liborc-0.4-0{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpng16-16{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqt5concurrent5{a} libqt5core5a{a} libqt5dbus5{a} libqt5designer5{a} libqt5designercomponents5{a} libqt5gui5{a} libqt5help5{a} libqt5network5{a} libqt5positioning5{a} libqt5printsupport5{a} libqt5qml5{a} libqt5qmlmodels5{a} libqt5quick5{a} libqt5quickwidgets5{a} libqt5sensors5{a} libqt5sql5{a} libqt5sql5-sqlite{a} libqt5test5{a} libqt5webchannel5{a} libqt5webkit5{a} libqt5widgets5{a} libqt5xml5{a} libreadline8{a} libsensors-config{a} libsensors5{a} libsm6{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libunwind8{a} libvulkan-dev{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwayland-server0{a} libwebp7{a} libwoff1{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-icccm4{a} libxcb-image0{a} libxcb-keysyms1{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render-util0{a} libxcb-render0{a} libxcb-shape0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-util1{a} libxcb-xfixes0{a} libxcb-xinerama0{a} libxcb-xinput0{a} libxcb-xkb1{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes3{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} qdoc-qt5{a} qhelpgenerator-qt5{a} qt5-assistant{a} qt5-qmake{a} qt5-qmake-bin{a} qtattributionsscanner-qt5{a} qtbase5-dev{a} qtbase5-dev-tools{a} qtchooser{a} qttools5-dev-tools{a} readline-common{a} sensible-utils{a} shared-mime-info{a} x11-common{a} x11proto-dev{a} xkb-data{a} xorg-sgml-doctools{a} xtrans-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus geoclue-2.0 gstreamer1.0-plugins-base libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libpam-cap libqt5opengl5-dev libqt5svg5 lynx mesa-vulkan-drivers qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xdg-user-dirs 0 packages upgraded, 190 newly installed, 0 to remove and 0 not upgraded. Need to get 147 MB of archives. After unpacking 643 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libdw1 amd64 0.188-2.1 [235 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libunwind8 amd64 1.6.2-3 [51.2 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libcap2-bin amd64 1:2.66-3 [34.6 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libgstreamer1.0-0 amd64 1.22.0-2 [1169 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 liborc-0.4-0 amd64 1:0.4.33-2 [164 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 iso-codes all 4.13.0-1 [2899 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libgstreamer-plugins-base1.0-0 amd64 1.22.0-3 [933 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libhyphen0 amd64 2.8.8-7 [32.5 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdouble-conversion3 amd64 3.2.1-1 [41.5 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libpcre2-16-0 amd64 10.42-1 [245 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libqt5core5a amd64 5.15.8+dfsg-3 [1808 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libwayland-server0 amd64 1.21.0-1 [35.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libgbm1 amd64 22.3.6-1+deb12u1 [38.0 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libwayland-client0 amd64 1.21.0-1 [28.3 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libegl-mesa0 amd64 22.3.6-1+deb12u1 [114 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libegl1 amd64 1.6.0-1 [33.7 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libevdev2 amd64 1.13.0+dfsg-1 [34.0 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libmtdev1 amd64 1.1.6-1 [23.0 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libgudev-1.0-0 amd64 237-2 [15.1 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libwacom-common all 2.6.0-1 [58.4 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libwacom9 amd64 2.6.0-1 [21.5 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libinput-bin amd64 1.22.1-1 [23.2 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libinput10 amd64 1.22.1-1 [125 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libmd4c0 amd64 0.4.8-1 [44.2 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libqt5dbus5 amd64 5.15.8+dfsg-3 [211 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libqt5network5 amd64 5.15.8+dfsg-3 [674 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libxcb-icccm4 amd64 0.4.1-1.1 [27.4 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libxcb-image0 amd64 0.4.0-2 [22.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libxcb-shape0 amd64 1.15-1 [106 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libxcb-xinerama0 amd64 1.15-1 [105 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libxcb-xinput0 amd64 1.15-1 [130 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libxcb-xkb1 amd64 1.15-1 [129 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 xkb-data all 2.35.1-1 [764 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libxkbcommon0 amd64 1.5.0-1 [106 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libxkbcommon-x11-0 amd64 1.5.0-1 [15.6 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libqt5gui5 amd64 5.15.8+dfsg-3 [3405 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libqt5positioning5 amd64 5.15.8+dfsg-2 [203 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-9 [107 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-9 [41.3 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-9 [45.1 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libqt5widgets5 amd64 5.15.8+dfsg-3 [2381 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libqt5printsupport5 amd64 5.15.8+dfsg-3 [201 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libqt5qml5 amd64 5.15.8+dfsg-3 [1356 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libqt5qmlmodels5 amd64 5.15.8+dfsg-3 [189 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libqt5quick5 amd64 5.15.8+dfsg-3 [1592 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libqt5sensors5 amd64 5.15.8-2 [112 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libqt5webchannel5 amd64 5.15.8-2 [58.2 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libwoff1 amd64 1.0.2-2 [43.0 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libqt5webkit5 amd64 5.212.0~alpha4-30 [11.9 MB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 124 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 147 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libllvm14 amd64 1:14.0.6-12 [21.8 MB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libclang1-14 amd64 1:14.0.6-12 [6157 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 x11proto-dev all 2022.1-1 [599 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libx11-dev amd64 2:1.8.4-2 [836 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libglx-dev amd64 1.6.0-1 [15.3 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libgl-dev amd64 1.6.0-1 [100 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libegl-dev amd64 1.6.0-1 [19.1 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libopengl0 amd64 1.6.0-1 [30.6 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libglu1-mesa amd64 9.0.2-1.1 [178 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libopengl-dev amd64 1.6.0-1 [4936 B] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1 [216 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libqt5concurrent5 amd64 5.15.8+dfsg-3 [41.7 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libqt5xml5 amd64 5.15.8+dfsg-3 [121 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libqt5designer5 amd64 5.15.8-2 [2748 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libqt5designercomponents5 amd64 5.15.8-2 [727 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libqt5sql5 amd64 5.15.8+dfsg-3 [121 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libqt5help5 amd64 5.15.8-2 [149 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libqt5quickwidgets5 amd64 5.15.8+dfsg-3 [39.4 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libqt5sql5-sqlite amd64 5.15.8+dfsg-3 [56.3 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libqt5test5 amd64 5.15.8+dfsg-3 [145 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libvulkan1 amd64 1.3.239.0-1 [116 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libvulkan-dev amd64 1.3.239.0-1 [1115 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 qtchooser amd64 66-2 [26.3 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 qdoc-qt5 amd64 5.15.8-2 [589 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 qhelpgenerator-qt5 amd64 5.15.8-2 [57.5 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 qt5-assistant amd64 5.15.8-2 [349 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 qt5-qmake-bin amd64 5.15.8+dfsg-3 [1023 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 qt5-qmake amd64 5.15.8+dfsg-3 [221 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 qtattributionsscanner-qt5 amd64 5.15.8-2 [30.7 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 qtbase5-dev-tools amd64 5.15.8+dfsg-3 [756 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 qtbase5-dev amd64 5.15.8+dfsg-3 [1121 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 qttools5-dev-tools amd64 5.15.8-2 [1029 kB] Fetched 147 MB in 2s (91.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libglib2.0-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../000-libglib2.0-0_2.74.6-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.6-2) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../001-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package libdw1:amd64. Preparing to unpack .../002-libdw1_0.188-2.1_amd64.deb ... Unpacking libdw1:amd64 (0.188-2.1) ... Selecting previously unselected package libunwind8:amd64. Preparing to unpack .../003-libunwind8_1.6.2-3_amd64.deb ... Unpacking libunwind8:amd64 (1.6.2-3) ... Selecting previously unselected package libcap2-bin. Preparing to unpack .../004-libcap2-bin_1%3a2.66-3_amd64.deb ... Unpacking libcap2-bin (1:2.66-3) ... Selecting previously unselected package libgstreamer1.0-0:amd64. Preparing to unpack .../005-libgstreamer1.0-0_1.22.0-2_amd64.deb ... Unpacking libgstreamer1.0-0:amd64 (1.22.0-2) ... Selecting previously unselected package liborc-0.4-0:amd64. Preparing to unpack .../006-liborc-0.4-0_1%3a0.4.33-2_amd64.deb ... Unpacking liborc-0.4-0:amd64 (1:0.4.33-2) ... Selecting previously unselected package iso-codes. Preparing to unpack .../007-iso-codes_4.13.0-1_all.deb ... Unpacking iso-codes (4.13.0-1) ... Selecting previously unselected package libgstreamer-plugins-base1.0-0:amd64. 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Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libgbm1:amd64 (22.3.6-1+deb12u1) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libqt5positioning5:amd64 (5.15.8+dfsg-2) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libx11-dev:amd64 (2:1.8.4-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libclang1-14 (1:14.0.6-12) ... Setting up libgstreamer-plugins-base1.0-0:amd64 (1.22.0-3) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libqt5network5:amd64 (5.15.8+dfsg-3) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... 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Setting up libgl-dev:amd64 (1.6.0-1) ... Setting up libvulkan-dev:amd64 (1.3.239.0-1) ... Setting up libegl-dev:amd64 (1.6.0-1) ... Setting up libqt5gui5:amd64 (5.15.8+dfsg-3) ... Setting up libqt5widgets5:amd64 (5.15.8+dfsg-3) ... Setting up libqt5help5:amd64 (5.15.8-2) ... Setting up libqt5printsupport5:amd64 (5.15.8+dfsg-3) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1) ... Setting up qtbase5-dev:amd64 (5.15.8+dfsg-3) ... Setting up libqt5quick5:amd64 (5.15.8+dfsg-3) ... Setting up libqt5designer5:amd64 (5.15.8-2) ... Setting up qhelpgenerator-qt5 (5.15.8-2) ... Setting up libqt5webkit5:amd64 (5.212.0~alpha4-30) ... Setting up libqt5designercomponents5:amd64 (5.15.8-2) ... Setting up libqt5quickwidgets5:amd64 (5.15.8+dfsg-3) ... Setting up qt5-assistant (5.15.8-2) ... Setting up qttools5-dev-tools (5.15.8-2) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/303538/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/303538/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/clustalx-2.1+lgpl/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../clustalx_2.1+lgpl-9_source.changes dpkg-buildpackage: info: source package clustalx dpkg-buildpackage: info: source version 2.1+lgpl-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory '/build/clustalx-2.1+lgpl' rm -f moc_* dh_clean make[1]: Leaving directory '/build/clustalx-2.1+lgpl' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/clustalx-2.1+lgpl' dh_auto_configure qmake -makefile "QMAKE_CFLAGS_RELEASE=-g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now" "QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now" QMAKE_STRIP=: PREFIX=/usr Info: creating stash file /build/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 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security:" \ -e "s:CXXFLAGS *= .*:& -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security:" \ -e "s:LFLAGS *= .*:& -Wl,-z,relro -Wl,-z,now:" Makefile make[1]: Leaving directory '/build/clustalx-2.1+lgpl' dh_auto_build make -j15 make[1]: Entering directory '/build/clustalx-2.1+lgpl' g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentWidget.o AlignmentWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignOutputFileNames.o AlignOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColorFileXmlParser.o ColorFileXmlParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] 74 | // tr("colorrules not found in the parameter file, using\ | ^ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'QColor ColorParameters::getResidueColor(QChar, QChar)': ColorParameters.cpp:160:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 160 | for(i = 0; i < colorPar.size(); i++) | ~~^~~~~~~~~~~~~~~~~ ColorParameters.cpp:174:26: warning: unused variable 'temp' [-Wunused-variable] 174 | char temp = colorPar[i].consensusConditionList[j].toLatin1(); | ^~~~ ColorParameters.cpp:157:10: warning: unused variable 'showRes' [-Wunused-variable] 157 | char showRes = res.toLatin1(); | ^~~~~~~ ColorParameters.cpp:158:10: warning: unused variable 'showCon' [-Wunused-variable] 158 | char showCon = consensus.toLatin1(); | ^~~~~~~ ColorParameters.cpp: In member function 'int ColorParameters::getResidueColorNum(QChar, QChar)': ColorParameters.cpp:197:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 197 | for(i = 0; i < colorPar.size(); i++) | ~~^~~~~~~~~~~~~~~~~ ColorParameters.cpp:211:26: warning: unused variable 'temp' [-Wunused-variable] 211 | char temp = colorPar[i].consensusConditionList[j].toLatin1(); | ^~~~ ColorParameters.cpp:194:10: warning: unused variable 'showRes' [-Wunused-variable] 194 | char showRes = res.toLatin1(); | ^~~~~~~ ColorParameters.cpp:195:10: warning: unused variable 'showCon' [-Wunused-variable] 195 | char showCon = consensus.toLatin1(); | ^~~~~~~ ColorParameters.cpp: In member function 'void ColorParameters::printColorInfo()': ColorParameters.cpp:229:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 229 | for(int i = 0; i < colors.size(); i++) | ~~^~~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'int ColorParameters::getIndexOfColor(QColor)': ColorParameters.cpp:238:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 238 | for(int i = 0; i < colors.size(); i++) | ~~^~~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'QColor ColorParameters::getColorFromNum(int)': ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 251 | if(colorNum > 0 && colorNum - 1 < colorPar.size()) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp In file included from main.cpp:21: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 106 | auto_ptr outFileNames; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from AlignOutputFileNames.cpp:16: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)': HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 180 | if(column >= 0 && column < arrayOfHeights->size()) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 198 | if(column >= 0 && column < arrayOfHeights->size()) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ HistogramWidget.cpp:208:47: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 208 | (fontMetrics.width(QString::number(rulerNum))) / 2; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qwidget.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qframe.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qlabel.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QLabel:1, from HistogramWidget.h:29, from HistogramWidget.cpp:23: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ HistogramWidget.cpp:241:61: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 241 | (fontMetrics.width(QString::number(0))) / 2, yPos, boxWidth, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ In file included from clustalW/Clustal.h:18, from mainwindow.h:45, from main.cpp:24: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qbrush.h:52, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpalette.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qwidget.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QWidget:1, from QTUtility.h:10, from main.cpp:22: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/Clustal.h:20: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from AlignmentParameters.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | 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] 48 | void AlignmentParameters::showEvent(QShowEvent* event) | ~~~~~~~~~~~~^~~~~ In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from LowScoringSegParams.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | 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] 85 | QTreeWidgetItem *parentItem) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] 51 | void LowScoringSegParams::showEvent(QShowEvent* event) | ~~~~~~~~~~~~^~~~~ ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)': ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] 138 | 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] 175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)': AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder] 170 | bool blackAndWhite; | ^~~~~~~~~~~~~ AlignmentWidget.h:161:27: warning: 'std::vector >* AlignmentWidget::selectedColoredRes' [-Wreorder] 161 | std::vector* selectedColoredRes; | ^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] 65 | AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) | ^~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calculatePixMaps()': AlignmentWidget.cpp:225:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 225 | for(unsigned int j = 0; j < lengthLongestSeq; j++) | ~~^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:235:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 235 | if(code >= 0 && code < conservationPixmaps->size()) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:268:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 268 | if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:280:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 280 | if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:291:86: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 291 | if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j) | ~~~~~~~~~~~~~~~~~~~~~^~~ AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable] 215 | int codeForSpace = clustalw::userParameters->resIndex( | ^~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::generateSecStructurePixmaps()': AlignmentWidget.cpp:333:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 333 | if(i < secStructPixmaps->size() && i < secStructInfo.size()) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:344:34: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 344 | fontMetrics.width(secStructInfo[i])/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QtGui:26, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from AlignmentWidget.cpp:48: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::drawContents(QPainter*, int, int, int, int)': AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 569 | if(selectedRes >= selectedColoredRes->size()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()': AlignmentWidget.cpp:689:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 689 | for(int j = 1; j <= strongGroup.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:693:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 693 | for(int j = 1; j <= weakGroup.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:700:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 700 | if((i + _fRes - 1 < (*alignment)[j].size()) && | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:701:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 701 | (i + _fRes - 1 < (*alignment)[_fSeq].size())) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:725:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 725 | for(int k = 1; k <= strongGroup.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:737:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 737 | for(int k = 1; k <= weakGroup.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:760:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 760 | for(int k = 1; k <= strongGroup.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:771:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 771 | 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 of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 878 | if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()': AlignmentWidget.cpp:927:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 927 | if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()': AlignmentWidget.cpp:1039:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1039 | for(int j = 0; j < aminoAcid.size(); j++) | ~~^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:1051:49: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1051 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp:1079:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1079 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp:1089:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1089 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp:1099:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1099 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp:1118:30: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1118 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr treeFileNames; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from BootstrapTreeDialog.cpp:8: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ HelpDisplayWidget.cpp: In member function 'std::string* HelpDisplayWidget::loadHelpInformation(char)': HelpDisplayWidget.cpp:147:29: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 147 | catch(ifstream::failure e) | ^ HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] 61 | int i, number, nlines; | ^~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdebug.h:54, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborcommon.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborvalue.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborarray.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:38, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from AlignmentViewerWidget.cpp:63: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 588 | for(i = 0; i < len && i < gapMask->size(); i++) | ~~^~~~~~~~~~~~~~~~~ AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 645 | for (i = 0; i < len && i < _secStructMask->size();i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 652 | 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] 781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) | ~~~~~~~~~~~~~~~^~~~~ In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from ColumnScoreParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | 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] 51 | void ColumnScoreParams::showEvent(QShowEvent* event) | ~~~~~~~~~~~~^~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from PairwiseParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | 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] 74 | void PairwiseParams::showEvent(QShowEvent* event) | ~~~~~~~~~~~~^~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/Clustal.h:18, from mainwindow.h:45: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdebug.h:54, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborcommon.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborvalue.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborarray.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:38, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from mainwindow.cpp:90: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/Clustal.h:20: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from mainwindow.cpp:99: WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 88 | auto_ptr params; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from mainwindow.cpp:100: AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 106 | auto_ptr outFileNames; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from mainwindow.cpp:101: TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 73 | auto_ptr treeFileNames; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from mainwindow.cpp:102: BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr treeFileNames; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ mainwindow.cpp: In member function 'virtual void MainWindow::showEvent(QShowEvent*)': mainwindow.cpp:198:40: warning: unused parameter 'event' [-Wunused-parameter] 198 | void MainWindow::showEvent(QShowEvent* event) | ~~~~~~~~~~~~^~~~~ mainwindow.cpp: In member function 'void MainWindow::writeViewer1AsPostscript(int)': mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] 1454 | void MainWindow::writeViewer1AsPostscript(int type) | ~~~~^~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/fileInput/FileReader.h:11: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/Clustal.h:20: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/Clustal.cpp:33: clustalW/tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/Clustal.cpp: In member function 'void clustalw::Clustal::align(std::string*, bool)': clustalW/Clustal.cpp:162:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 162 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/Clustal.cpp: In member function 'void clustalw::Clustal::doAlignUseOldTree(std::string*)': clustalW/Clustal.cpp:837:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 837 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -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, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()': clustalW/alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 47 | register int sl; /* which have code = gap_pos2 */ | ^~ clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()': clustalW/alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 122 | register int sl; /* which have code = gap_pos2 */ | ^~ clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()': clustalW/alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 617 | register int sl; | ^~ 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] 1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin(); | ^~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/alignment/AlignmentOutput.h:20: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp clustalW/alignment/AlignmentOutput.cpp:512:40: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 512 | bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.cpp:535:40: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 535 | string AlignmentOutput::openOutputFile(auto_ptr& outFile, string prompt, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:673:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 673 | catch(VectorOutOfRange e) | ^ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:868:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 868 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1027:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 1027 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1156:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 1156 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1445:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 1445 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1560:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 1560 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:2095:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 2095 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 2102 | catch(exception e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)': clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 2351 | catch(VectorOutOfRange e) | ^ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 207 | if(res.isLetter() && resNumber.size() > i - data->firstSeq) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 307 | if(res.isLetter() && resNumber.size() > seq) | ~~~~~~~~~~~~~~~~~^~~~~ PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 421 | if(res.isLetter() && resNumber.size() > i) | ~~~~~~~~~~~~~~~~~^~~ PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] 55 | int err; | ^~~ PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] 73 | int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local | ^~~~~~~ PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] 74 | 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 of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 587 | if(data->nameHeader.size() > ix) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 730 | 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 of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 789 | for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] 781 | int psX, psY, curveBottom; | ^~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from SaveSeqFile.cpp:14: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp clustalW/fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()': clustalW/fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 37 | register int i; | ^ clustalW/fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 38 | register char c; | ^ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | 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] 375 | QRect redrawRect = event->rect(); | ^~~~~~~~~~ SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()': SeqNameWidget.cpp:443:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 443 | int length = fontMetrics.width(QString(name.c_str())); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QtGui:26, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from SeqNameWidget.cpp:58: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/fileInput/FileReader.h:11: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)': clustalW/fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 155 | auto_ptr fileParser; // Means we dont need to delete it! | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 426 | void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/fileInput/FileReader.cpp: In member function 'void clustalw::FileReader::checkInfile(int*, std::auto_ptr&)': clustalW/fileInput/FileReader.cpp:555:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 555 | catch(exception ex) | ^~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 73 | auto_ptr treeFileNames; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from TreeOutputFileNames.cpp:7: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 88 | auto_ptr params; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from WritePostscriptFile.cpp:14: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual std::vector clustalw::MSFFileParser::getSeqRange(int, int, std::string*)': clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter] 34 | 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::string&, int&, int)': clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] 246 | void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] 246 | void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter] 247 | string& secStructName, int &structPenalties, int length) | ~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter] 247 | string& secStructName, int &structPenalties, int length) | ~~~~^~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp In file included from clustalW/general/OutputFile.cpp:9: clustalW/general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/general/OutputFile.h:8: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp clustalW/fileInput/PIRFileParser.cpp: In member function 'virtual void clustalw::PIRFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] 292 | void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:292:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] 292 | void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:293:45: warning: unused parameter 'secStructName' [-Wunused-parameter] 293 | string& secStructName, int &structPenalties, int length) | ~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter] 293 | string& secStructName, int &structPenalties, int length) | ~~~~^~~~~~ clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::string*)': clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter] 199 | Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) | ~~~~~~~~^~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] 444 | void PearsonFileParser::getSecStructure(vector& gapPenaltyMask, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter] 445 | vector& secStructMask, string& secStructName, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter] 445 | vector& secStructMask, string& secStructName, | ~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] 446 | int &structPenalties, int length) | ~~~~^~~~~~ clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector&, std::vector&, std::string&, int&, int)': clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] 240 | void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clustalW/general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const': clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript 1 is above array bounds of 'char [1]' [-Warray-bounds] 106 | delim[1] = 0; | ~~~~~~~^ clustalW/general/ClustalWResources.cpp:104:10: note: while referencing 'delim' 104 | char delim[1]; | ^~~~~ clustalW/general/ClustalWResources.cpp:105:14: warning: writing 2 bytes into a region of size 1 [-Wstringop-overflow=] 105 | delim[0] = DIRDELIM; | ~~~~~~~~~^~~~~~~~~~ clustalW/general/ClustalWResources.cpp:104:10: note: destination object 'delim' of size 1 104 | char delim[1]; | ^~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp clustalW/general/UserParameters.cpp: In constructor 'clustalw::UserParameters::UserParameters(bool)': clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter] 33 | UserParameters::UserParameters(bool log) | ~~~~~^~~ clustalW/general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)': clustalW/general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 475 | register int i; | ^ clustalW/general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)': clustalW/general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 53 | register int p; | ^ 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] 251 | 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] 519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) | ~~~~~~~~^~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp 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] 183 | 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] 221 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/interface/../fileInput/FileReader.h:11: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20: clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()': clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 41 | catch(bad_alloc) | ^~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/interface/../fileInput/FileReader.h:11: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20: clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ 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=] 520 | clustalObj->getHelp('C'); | ~~~~~~~~~~~~~~~~~~~^~~~~ clustalW/interface/InteractiveMenu.cpp:521:13: note: here 521 | 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] 1190 | system(lin1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/multipleAlign/../tree/TreeInterface.h:17: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ 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] 170 | int count; | ^~~~~ 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] 340 | 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::string)': clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] 359 | string phylipName) | ~~~~~~~^~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 231 | tmpnam (buffer); | ~~~~~~~^~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp 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] 1613 | void SubMatrix::tempInterface(int alignResidueType, int alignType) | ~~~~^~~~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp:1613:57: warning: unused parameter 'alignType' [-Wunused-parameter] 1613 | 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] 1657 | 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] 1717 | int maxRes; | ^~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp In file included from clustalW/tree/ClusterTree.h:23: clustalW/tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/tree/ClusterTree.h:16: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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] 580 | int rs = 0, rl = 0; | ^~ clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] 580 | int rs = 0, rl = 0; | ^~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp clustalW/tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)': clustalW/tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 164 | register int i; | ^ In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/tree/Tree.h:15: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 278 | auto_ptr Tree::createSets(int firstSeq, int lastSeq) | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 280 | auto_ptr progAlignSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ g++ -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -dM -E -o moc_predefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/features/data/dummy.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | 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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentFormatOptions.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp clustalW/tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/tree/TreeInterface.h:17: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp In file included from clustalW/tree/ClusterTree.h:23, 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:18: clustalW/tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:23: clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.cpp:31:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | auto_ptr | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.cpp:103:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 103 | auto_ptr | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.cpp:195:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 195 | auto_ptr | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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::string*, bool*)': clustalW/tree/TreeInterface.cpp:200:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 200 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 208 | auto_ptr | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::string*, std::vector*, int, int, bool*)': clustalW/tree/TreeInterface.cpp:214:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 214 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 439 | auto_ptr | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::string*, std::vector*, int, int, bool*)': clustalW/tree/TreeInterface.cpp:445:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 445 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 485 | auto_ptr | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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::string*, bool*)': clustalW/tree/TreeInterface.cpp:490:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 490 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 503 | auto_ptr TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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::string*, bool*)': clustalW/tree/TreeInterface.cpp:506:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 506 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/tree/UPGMA/../ClusterTree.h:23: clustalW/tree/UPGMA/../../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/tree/UPGMA/../ClusterTree.h:16: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/UPGMA/../ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11: clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 51 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 17 | auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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::string&)': clustalW/tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 21 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23: clustalW/tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/tree/ClusterTree.h:16: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | 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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, 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] 96 | 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] 97 | 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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include ColumnScoreParams.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include FileDialog.h -o moc_FileDialog.cpp clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:10: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 51 | auto_ptr progSteps; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 27 | auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ 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 [-Wmaybe-uninitialized] 1103 | return (maxRes); | ^ clustalW/substitutionMatrix/SubMatrix.cpp:998:9: note: 'n' was declared here 998 | int n, llimit, ulimit; | ^ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include HistogramWidget.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include LowScoringSegParams.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include mainwindow.h -o moc_mainwindow.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include PairwiseParams.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include ProteinGapParameters.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include PSPrinter.h -o moc_PSPrinter.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include SearchForString.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include SecStructOptions.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include SeqNameWidget.h -o moc_SeqNameWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include TreeFormatOptions.h -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 /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/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++/12 -I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/x86_64-linux-gnu/12/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include WritePostscriptFile.h -o moc_WritePostscriptFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from moc_AlignmentViewerWidget.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -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, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HelpDisplayWidget.h:18, from moc_HelpDisplayWidget.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, from moc_AlignmentWidget.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from BootstrapTreeDialog.h:11, from moc_BootstrapTreeDialog.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from AlignOutputFileNames.h:10, from moc_AlignOutputFileNames.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 106 | auto_ptr outFileNames; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from moc_AlignOutputFileNames.cpp:9: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr treeFileNames; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from moc_BootstrapTreeDialog.cpp:9: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/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 -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. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp In file included from clustalW/Clustal.h:18, from mainwindow.h:45: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from moc_mainwindow.cpp:9: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/Clustal.h:20: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from moc_SaveSeqFile.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, 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:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from moc_SeqNameWidget.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from TreeOutputFileNames.h:10, from moc_TreeOutputFileNames.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 73 | auto_ptr treeFileNames; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from moc_TreeOutputFileNames.cpp:9: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from WritePostscriptFile.h:10, from moc_WritePostscriptFile.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 88 | auto_ptr params; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from moc_WritePostscriptFile.cpp:9: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -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 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so /usr/lib/x86_64-linux-gnu/libQt5Gui.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so /usr/lib/x86_64-linux-gnu/libQt5Core.so -lGL -lpthread /usr/bin/ld: 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 '/build/clustalx-2.1+lgpl' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/clustalx/ dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/clustalx-2.1+lgpl' dh_installchangelogs debian/CHANGELOG.upstream make[1]: Leaving directory '/build/clustalx-2.1+lgpl' dh_installman dh_installmime dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-9_amd64.deb'. dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../clustalx_2.1+lgpl-9_amd64.buildinfo dpkg-genchanges --build=binary -O../clustalx_2.1+lgpl-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/303538/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/303538/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/303538 and its subdirectories I: Current time: Tue Apr 18 23:23:23 +14 2023 I: pbuilder-time-stamp: 1681809803