I: pbuilder: network access will be disabled during build I: Current time: Wed May 8 05:06:10 +14 2024 I: pbuilder-time-stamp: 1715094370 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 Fri Dec 4 22:20:42 2020 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/3072304/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. 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 May 7 15:06 /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/3072304/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3072304/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=302e41228fe74f42b9a72561bd7ee58c LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=3072304 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.ZjvCbPgw/pbuilderrc_fULq --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZjvCbPgw/b2 --logfile b2/build.log clustalx_2.1+lgpl-9.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 6 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3072304/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: arm64 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 ... 19743 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} fonts-dejavu-mono{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} libclang1-15t64{a} libcom-err2{a} libcups2t64{a} libdbus-1-3{a} libdebhelper-perl{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdw1t64{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libelf1t64{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} libglib2.0-0t64{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm15t64{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libmd4c0{a} libmtdev1t64{a} libopengl-dev{a} libopengl0{a} liborc-0.4-0t64{a} libpcre2-16-0{a} libpipeline1{a} libpng16-16t64{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqt5concurrent5t64{a} libqt5core5t64{a} libqt5dbus5t64{a} libqt5designer5{a} libqt5designercomponents5{a} libqt5gui5t64{a} libqt5help5{a} libqt5network5t64{a} libqt5positioning5{a} libqt5printsupport5t64{a} libqt5qml5{a} libqt5qmlmodels5{a} libqt5quick5{a} libqt5quickwidgets5{a} libqt5sensors5{a} libqt5sql5-sqlite{a} libqt5sql5t64{a} libqt5test5t64{a} libqt5webchannel5{a} libqt5webkit5{a} libqt5widgets5t64{a} libqt5xml5t64{a} libreadline8t64{a} libsensors-config{a} libsensors5{a} libsharpyuv0{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} netbase{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} tzdata{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 krb5-locales 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, 198 newly installed, 0 to remove and 0 not upgraded. Need to get 142 MB of archives. After unpacking 678 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.78.4-7 [1364 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 3 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libdw1t64 arm64 0.191-1+b1 [230 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libunwind8 arm64 1.6.2-3+b1 [47.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libcap2-bin arm64 1:2.66-5 [34.0 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libgstreamer1.0-0 arm64 1.24.2-1 [1245 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 liborc-0.4-0t64 arm64 1:0.4.38-1 [172 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 iso-codes all 4.16.0-1 [2936 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libgstreamer-plugins-base1.0-0 arm64 1.24.3-1 [883 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libhyphen0 arm64 2.8.8-7+b1 [30.3 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 shared-mime-info arm64 2.4-4 [755 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libdouble-conversion3 arm64 3.3.0-1+b1 [37.0 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libpcre2-16-0 arm64 10.42-4+b1 [217 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libqt5core5t64 arm64 5.15.10+dfsg-7.2+b1 [1700 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libglvnd0 arm64 1.7.0-1+b1 [41.7 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libwayland-server0 arm64 1.22.0-2.1+b1 [32.3 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libgbm1 arm64 23.3.5-1 [39.7 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libglapi-mesa arm64 23.3.5-1 [45.5 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libwayland-client0 arm64 1.22.0-2.1+b1 [24.8 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libx11-xcb1 arm64 2:1.8.7-1+b1 [232 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libxcb-present0 arm64 1.15-1 [106 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libxshmfence1 arm64 1.3-1+b1 [9080 B] Get: 48 http://deb.debian.org/debian trixie/main arm64 libegl-mesa0 arm64 23.3.5-1 [111 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libegl1 arm64 1.7.0-1+b1 [33.9 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libxfixes3 arm64 1:6.0.0-2+b1 [20.5 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libvulkan1 arm64 1.3.280.0-1 [119 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [18.7 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libdrm-radeon1 arm64 2.4.120-2 [21.1 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-11 [21.3 MB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libsensors5 arm64 1:3.6.0-9 [33.9 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libgl1-mesa-dri arm64 23.3.5-1 [6928 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libglx-mesa0 arm64 23.3.5-1 [150 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libglx0 arm64 1.7.0-1+b1 [31.0 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libgl1 arm64 1.7.0-1+b1 [90.9 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libevdev2 arm64 1.13.1+dfsg-1+b1 [31.0 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libmtdev1t64 arm64 1.1.6-1.2 [21.9 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libgudev-1.0-0 arm64 238-5 [13.6 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libwacom-common all 2.10.0-2 [62.5 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libwacom9 arm64 2.10.0-2 [21.5 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libinput-bin arm64 1.25.0-1+b2 [24.8 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libinput10 arm64 1.25.0-1+b2 [116 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libmd4c0 arm64 0.4.8-1+b1 [42.2 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libdbus-1-3 arm64 1.14.10-4+b1 [195 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libqt5dbus5t64 arm64 5.15.10+dfsg-7.2+b1 [205 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 86 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libqt5network5t64 arm64 5.15.10+dfsg-7.2+b1 [653 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libxcb-icccm4 arm64 0.4.1-1.1+b1 [26.5 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libxcb-util1 arm64 0.4.0-1+b1 [23.2 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libxcb-image0 arm64 0.4.0-2+b1 [22.0 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libxcb-keysyms1 arm64 0.4.0-1+b2 [16.0 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libxcb-render-util0 arm64 0.3.9-1+b1 [17.5 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libxcb-shape0 arm64 1.15-1 [106 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libxcb-xinerama0 arm64 1.15-1 [105 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libxcb-xinput0 arm64 1.15-1 [130 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxcb-xkb1 arm64 1.15-1 [128 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 xkb-data all 2.41-2 [795 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libxkbcommon0 arm64 1.6.0-1+b1 [103 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libxkbcommon-x11-0 arm64 1.6.0-1+b1 [15.4 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libqt5gui5t64 arm64 5.15.10+dfsg-7.2+b1 [3134 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libqt5positioning5 arm64 5.15.10+dfsg-3+b2 [191 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libavahi-common-data arm64 0.8-13+b2 [112 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libavahi-common3 arm64 0.8-13+b2 [42.4 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libavahi-client3 arm64 0.8-13+b2 [45.7 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libcups2t64 arm64 2.4.7-1.2+b1 [230 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libqt5widgets5t64 arm64 5.15.10+dfsg-7.2+b1 [2263 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libqt5printsupport5t64 arm64 5.15.10+dfsg-7.2+b1 [197 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libqt5qml5 arm64 5.15.10+dfsg-2+b2 [1285 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libqt5qmlmodels5 arm64 5.15.10+dfsg-2+b2 [184 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libqt5quick5 arm64 5.15.10+dfsg-2+b2 [1512 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libqt5sensors5 arm64 5.15.10-2+b2 [110 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libqt5webchannel5 arm64 5.15.10-2+b2 [57.0 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.3.2-0.4+b1 [107 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.3.2-0.4+b1 [263 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libwoff1 arm64 1.0.2-2+b1 [41.7 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1+b1 [221 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libqt5webkit5 arm64 5.212.0~alpha4-33+b3 [10.3 MB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 133 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 156 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libllvm15t64 arm64 1:15.0.7-14+b1 [20.8 MB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libclang1-15t64 arm64 1:15.0.7-14+b1 [5755 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 x11proto-dev all 2024.1-1 [603 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libxau-dev arm64 1:1.0.9-1+b1 [21.5 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libxdmcp-dev arm64 1:1.1.2-3+b1 [40.6 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libpthread-stubs0-dev arm64 0.4-1+b1 [5324 B] Get: 169 http://deb.debian.org/debian trixie/main arm64 libxcb1-dev arm64 1.15-1 [182 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libx11-dev arm64 2:1.8.7-1+b1 [861 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 libglx-dev arm64 1.7.0-1+b1 [15.8 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 libgl-dev arm64 1.7.0-1+b1 [101 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 libegl-dev arm64 1.7.0-1+b1 [19.5 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libopengl0 arm64 1.7.0-1+b1 [32.1 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libglu1-mesa arm64 9.0.2-1.1+b1 [156 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libopengl-dev arm64 1.7.0-1+b1 [5372 B] Get: 177 http://deb.debian.org/debian trixie/main arm64 libglu1-mesa-dev arm64 9.0.2-1.1+b1 [196 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libqt5concurrent5t64 arm64 5.15.10+dfsg-7.2+b1 [43.7 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libqt5xml5t64 arm64 5.15.10+dfsg-7.2+b1 [121 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libqt5designer5 arm64 5.15.10-7 [2717 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libqt5designercomponents5 arm64 5.15.10-7 [700 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 libqt5sql5t64 arm64 5.15.10+dfsg-7.2+b1 [120 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libqt5help5 arm64 5.15.10-7 [144 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libqt5quickwidgets5 arm64 5.15.10+dfsg-2+b2 [39.5 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libqt5sql5-sqlite arm64 5.15.10+dfsg-7.2+b1 [57.6 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libqt5test5t64 arm64 5.15.10+dfsg-7.2+b1 [138 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libvulkan-dev arm64 1.3.280.0-1 [1348 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libxext-dev arm64 2:1.3.4-1+b1 [107 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 qtchooser arm64 66-2 [24.9 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 qdoc-qt5 arm64 5.15.10-7 [547 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 qhelpgenerator-qt5 arm64 5.15.10-7 [56.4 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 qt5-assistant arm64 5.15.10-7 [347 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 qt5-qmake-bin arm64 5.15.10+dfsg-7.2+b1 [910 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 qt5-qmake arm64 5.15.10+dfsg-7.2+b1 [223 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 qtattributionsscanner-qt5 arm64 5.15.10-7 [30.3 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 qtbase5-dev-tools arm64 5.15.10+dfsg-7.2+b1 [714 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 qtbase5-dev arm64 5.15.10+dfsg-7.2+b1 [1119 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 qttools5-dev-tools arm64 5.15.10-7 [1002 kB] Fetched 142 MB in 1s (195 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libglib2.0-0t64:arm64. (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 ... 19743 files and directories currently installed.) Preparing to unpack .../000-libglib2.0-0t64_2.78.4-7_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.78.4-7) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../001-libdrm-common_2.4.120-2_all.deb ... Unpacking libdrm-common (2.4.120-2) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../002-libdrm2_2.4.120-2_arm64.deb ... Unpacking libdrm2:arm64 (2.4.120-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../003-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package libdw1t64:arm64. Preparing to unpack .../004-libdw1t64_0.191-1+b1_arm64.deb ... Unpacking libdw1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package libunwind8:arm64. Preparing to unpack .../005-libunwind8_1.6.2-3+b1_arm64.deb ... Unpacking libunwind8:arm64 (1.6.2-3+b1) ... Selecting previously unselected package libcap2-bin. Preparing to unpack .../006-libcap2-bin_1%3a2.66-5_arm64.deb ... Unpacking libcap2-bin (1:2.66-5) ... Selecting previously unselected package libgstreamer1.0-0:arm64. Preparing to unpack .../007-libgstreamer1.0-0_1.24.2-1_arm64.deb ... Unpacking libgstreamer1.0-0:arm64 (1.24.2-1) ... Selecting previously unselected package liborc-0.4-0t64:arm64. Preparing to unpack .../008-liborc-0.4-0t64_1%3a0.4.38-1_arm64.deb ... Unpacking liborc-0.4-0t64:arm64 (1:0.4.38-1) ... Selecting previously unselected package iso-codes. Preparing to unpack .../009-iso-codes_4.16.0-1_all.deb ... Unpacking iso-codes (4.16.0-1) ... Selecting previously unselected package libgstreamer-plugins-base1.0-0:arm64. Preparing to unpack .../010-libgstreamer-plugins-base1.0-0_1.24.3-1_arm64.deb ... Unpacking libgstreamer-plugins-base1.0-0:arm64 (1.24.3-1) ... Selecting previously unselected package libhyphen0:arm64. Preparing to unpack .../011-libhyphen0_2.8.8-7+b1_arm64.deb ... Unpacking libhyphen0:arm64 (2.8.8-7+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../012-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../013-libjpeg62-turbo_1%3a2.1.5-3_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../014-libpng16-16t64_1.6.43-5_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.43-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../015-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../016-shared-mime-info_2.4-4_arm64.deb ... Unpacking shared-mime-info (2.4-4) ... Selecting previously unselected package libdouble-conversion3:arm64. Preparing to unpack .../017-libdouble-conversion3_3.3.0-1+b1_arm64.deb ... Unpacking libdouble-conversion3:arm64 (3.3.0-1+b1) ... Selecting previously unselected package libpcre2-16-0:arm64. Preparing to unpack .../018-libpcre2-16-0_10.42-4+b1_arm64.deb ... Unpacking libpcre2-16-0:arm64 (10.42-4+b1) ... Selecting previously unselected package libqt5core5t64:arm64. Preparing to unpack .../019-libqt5core5t64_5.15.10+dfsg-7.2+b1_arm64.deb ... Unpacking libqt5core5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../020-libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../021-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../022-libfreetype6_2.13.2+dfsg-1+b4_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../023-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../024-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../025-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../026-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../027-fontconfig_2.15.0-1.1_arm64.deb ... Unpacking fontconfig (2.15.0-1.1) ... Selecting previously unselected package libglvnd0:arm64. Preparing to unpack .../028-libglvnd0_1.7.0-1+b1_arm64.deb ... Unpacking libglvnd0:arm64 (1.7.0-1+b1) ... Selecting previously unselected package libwayland-server0:arm64. Preparing to unpack .../029-libwayland-server0_1.22.0-2.1+b1_arm64.deb ... Unpacking libwayland-server0:arm64 (1.22.0-2.1+b1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../030-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../031-libbsd0_0.12.2-1_arm64.deb ... Unpacking libbsd0:arm64 (0.12.2-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../032-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../033-libxcb1_1.15-1_arm64.deb ... Unpacking libxcb1:arm64 (1.15-1) ... Selecting previously unselected package libxcb-randr0:arm64. Preparing to unpack .../034-libxcb-randr0_1.15-1_arm64.deb ... Unpacking libxcb-randr0:arm64 (1.15-1) ... Selecting previously unselected package libgbm1:arm64. Preparing to unpack .../035-libgbm1_23.3.5-1_arm64.deb ... Unpacking libgbm1:arm64 (23.3.5-1) ... Selecting previously unselected package libglapi-mesa:arm64. Preparing to unpack .../036-libglapi-mesa_23.3.5-1_arm64.deb ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... 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Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-9) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up xkb-data (2.41-2) ... Setting up libcom-err2:arm64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libunwind8:arm64 (1.6.2-3+b1) ... Setting up libpthread-stubs0-dev:arm64 (0.4-1+b1) ... Setting up libpcre2-16-0:arm64 (10.42-4+b1) ... Setting up libopengl0:arm64 (1.7.0-1+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up liborc-0.4-0t64:arm64 (1:0.4.38-1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libdw1t64:arm64 (0.191-1+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue May 7 15:06:38 UTC 2024. Universal Time is now: Tue May 7 15:06:38 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. 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Setting up libwayland-client0:arm64 (1.22.0-2.1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:arm64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libxcb-xfixes0:arm64 (1.15-1) ... Setting up libxau-dev:arm64 (1:1.0.9-1+b1) ... Setting up qt5-qmake:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libxcb-xinput0:arm64 (1.15-1) ... Setting up libwoff1:arm64 (1.0.2-2+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up libwacom9:arm64 (2.10.0-2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:arm64 (1.15-1) ... Setting up libedit2:arm64 (3.1-20230828-1+b1) ... Setting up libxcb-keysyms1:arm64 (0.4.0-1+b2) ... Setting up libxcb-shape0:arm64 (1.15-1) ... Setting up libavahi-common3:arm64 (0.8-13+b2) ... Setting up libxcb-render-util0:arm64 (0.3.9-1+b1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libxcb-icccm4:arm64 (0.4.1-1.1+b1) ... Setting up libxcb-util1:arm64 (0.4.0-1+b1) ... Setting up libinput-bin (1.25.0-1+b2) ... Setting up libxcb-xkb1:arm64 (1.15-1) ... Setting up libxcb-image0:arm64 (0.4.0-2+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:arm64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:arm64 (1:1.1.2-3+b1) ... Setting up libxcb-xinerama0:arm64 (1.15-1) ... Setting up libllvm17t64:arm64 (1:17.0.6-11) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:arm64 (1.15-1) ... Setting up shared-mime-info (2.4-4) ... Setting up libxkbcommon-x11-0:arm64 (1.6.0-1+b1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up libxcb-dri2-0:arm64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:arm64 (2.4.120-2) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:arm64 (1.15-1) ... Setting up libxslt1.1:arm64 (1.1.35-1+b1) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libsm6:arm64 (2:1.2.3-1+b1) ... Setting up libavahi-client3:arm64 (0.8-13+b2) ... Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... Setting up libxcb-dri3-0:arm64 (1.15-1) ... Setting up libinput10:arm64 (1.25.0-1+b2) ... Setting up libx11-xcb1:arm64 (2:1.8.7-1+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... Setting up libxcb1-dev:arm64 (1.15-1) ... Setting up libllvm15t64:arm64 (1:15.0.7-14+b1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libgbm1:arm64 (23.3.5-1) ... Setting up libdrm-radeon1:arm64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libgl1-mesa-dri:arm64 (23.3.5-1) ... Setting up libx11-dev:arm64 (2:1.8.7-1+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libgstreamer-plugins-base1.0-0:arm64 (1.24.3-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up libqt5core5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libegl-mesa0:arm64 (23.3.5-1) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b1) ... Setting up qtattributionsscanner-qt5 (5.15.10-7) ... Setting up libclang1-15t64 (1:15.0.7-14+b1) ... Setting up libxext-dev:arm64 (2:1.3.4-1+b1) ... Setting up libegl1:arm64 (1.7.0-1+b1) ... Setting up libqt5sql5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libcups2t64:arm64 (2.4.7-1.2+b1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libqt5dbus5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libglx-mesa0:arm64 (23.3.5-1) ... Setting up libqt5sql5-sqlite:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libglx0:arm64 (1.7.0-1+b1) ... Setting up qdoc-qt5 (5.15.10-7) ... Setting up libqt5concurrent5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libqt5positioning5:arm64 (5.15.10+dfsg-3+b2) ... Setting up libqt5network5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libqt5xml5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libqt5test5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up qtbase5-dev-tools (5.15.10+dfsg-7.2+b1) ... Setting up libgl1:arm64 (1.7.0-1+b1) ... Setting up libqt5qml5:arm64 (5.15.10+dfsg-2+b2) ... Setting up libqt5webchannel5:arm64 (5.15.10-2+b2) ... Setting up libglx-dev:arm64 (1.7.0-1+b1) ... Setting up libqt5sensors5:arm64 (5.15.10-2+b2) ... Setting up libgl-dev:arm64 (1.7.0-1+b1) ... Setting up libvulkan-dev:arm64 (1.3.280.0-1) ... Setting up libqt5qmlmodels5:arm64 (5.15.10+dfsg-2+b2) ... Setting up libegl-dev:arm64 (1.7.0-1+b1) ... Setting up libqt5gui5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libglu1-mesa-dev:arm64 (9.0.2-1.1+b1) ... Setting up libqt5quick5:arm64 (5.15.10+dfsg-2+b2) ... Setting up libqt5widgets5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libqt5help5:arm64 (5.15.10-7) ... Setting up libqt5quickwidgets5:arm64 (5.15.10+dfsg-2+b2) ... Setting up libqt5printsupport5t64:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up libqt5designer5:arm64 (5.15.10-7) ... Setting up qhelpgenerator-qt5 (5.15.10-7) ... Setting up libqt5webkit5:arm64 (5.212.0~alpha4-33+b3) ... Setting up libqt5designercomponents5:arm64 (5.15.10-7) ... Setting up qtbase5-dev:arm64 (5.15.10+dfsg-7.2+b1) ... Setting up qt5-assistant (5.15.10-7) ... Setting up qttools5-dev-tools (5.15.10-7) ... Processing triggers for libc-bin (2.38-7) ... 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 I: Building the package I: user script /srv/workspace/pbuilder/3072304/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3072304/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/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 arm64 debian/rules clean dh clean dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/clustalx-2.1+lgpl' rm -f moc_* dh_clean make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/clustalx-2.1+lgpl' dh_auto_configure qmake -makefile "QMAKE_CFLAGS_RELEASE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard:" \ -e "s:CXXFLAGS *= .*:& -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard:" \ -e "s:LFLAGS *= .*:& -Wl,-z,relro -Wl,-z,now:" Makefile make[1]: Leaving directory '/build/reproducible-path/clustalx-2.1+lgpl' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/clustalx-2.1+lgpl' g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentWidget.o AlignmentWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignOutputFileNames.o AlignOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ColorFileXmlParser.o ColorFileXmlParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.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 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++) | ~~^~~~~~~~~~~~~~~ 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"); | ^~~~~~~~~~~~~~ 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()) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp 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"); | ^~~~~~~~~~~~~~ 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/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"); | ^~~~~~~~~~~~~~ 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/aarch64-linux-gnu/qt5/QtGui/QtGui:26, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from AlignmentWidget.cpp:48: /usr/include/aarch64-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)) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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"); | ^~~~~~~~~~~~~~ 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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ 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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QPushButton:1, from AlignOutputFileNames.cpp:16: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ AlignmentWidget.cpp:1118:30: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1118 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ 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; | ^~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-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 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"); | ^~~~~~~~~~~~~~ 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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdebug.h:54, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborcommon.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborvalue.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborarray.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QtCore:38, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from AlignmentViewerWidget.cpp:63: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/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"); | ^~~~~~~~~~~~~~ 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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QPushButton:1, from BootstrapTreeDialog.cpp:8: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp 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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.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 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"); | ^~~~~~~~~~~~~~ ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)': ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] 85 | QTreeWidgetItem *parentItem) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 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) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qbrush.h:52, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpalette.h:46, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QWidget:1, from QTUtility.h:10, from main.cpp:22: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp 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/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qframe.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qlabel.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QLabel:1, from HistogramWidget.h:29, from HistogramWidget.cpp:23: /usr/include/aarch64-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/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp 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"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp 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"); | ^~~~~~~~~~~~~~ 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) | ~~~~~~~~~~~~^~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp 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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdebug.h:54, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborcommon.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborvalue.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qcborarray.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QtCore:38, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from mainwindow.cpp:90: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.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++/13/memory:78, from clustalW/fileInput/FileReader.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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"); | ^~~~~~~~~~~~~~ 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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) | ~~~~~~~~~~~~^~~~~ 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.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) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QPushButton:1, from SaveSeqFile.cpp:14: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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(); | ^~~~~~~~~~ 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; | ^~~ 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/aarch64-linux-gnu/qt5/QtGui/QtGui:26, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from SeqNameWidget.cpp:58: /usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp 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++/13/memory:78, from clustalW/alignment/AlignmentOutput.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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) | ^ 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) | ^ 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"); | ^~~~~~~~~~~~~~ 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/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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QPushButton:1, from TreeOutputFileNames.cpp:7: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp 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++/13/memory:78, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QPushButton:1, from WritePostscriptFile.cpp:14: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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/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++/13/memory:78, from clustalW/fileInput/FileReader.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp 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/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) | ~~~~^~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.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++/13/memory:78, from clustalW/general/OutputFile.h:8: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp 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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.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"); | ^~~~~~~~~~~~~~ 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) | ~~~~~~~~^~~~~~~~~~~~~ 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 '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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.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++/13/memory:78, from clustalW/interface/../fileInput/FileReader.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp 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/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"); | ^~~~~~~~~~~~~~ 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/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++/13/memory:78, from clustalW/multipleAlign/../tree/TreeInterface.h:17: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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++/13/memory:78, from clustalW/interface/../fileInput/FileReader.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] 170 | int count; | ^~~~~ 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) | ^~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp 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"); | ^~~~~~~~~~~~~~ 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/ProfileBase.cpp: In member function 'void clustalw::ProfileBase::calcResidueSpecificPen(clustalw::SeqArray*, std::vector*)': clustalW/multipleAlign/ProfileBase.cpp:372:25: warning: comparison is always false due to limited range of data type [-Wtype-limits] 372 | if ((ix < 0) || (ix > _maxAA)) | ~~~^~~ 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/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/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"); | ^~~~~~~~~~~~~~ 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); | ~~~~~~~^~~~~~~~ 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': | ^~~~ 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"); | ^~~~~~~~~~~~~~ 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/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/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/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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.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"); | ^~~~~~~~~~~~~~ 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++/13/memory:78, from clustalW/tree/ClusterTree.h:16: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.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/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"); | ^~~~~~~~~~~~~~ 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++/13/memory:78, from clustalW/tree/TreeInterface.h:17: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/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"); | ^~~~~~~~~~~~~~ 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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++/13/memory:78, from clustalW/tree/Tree.h:15: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.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/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"); | ^~~~~~~~~~~~~~ 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++/13/memory:78, from clustalW/tree/ClusterTree.h:16: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/memory:78, from clustalW/tree/UPGMA/../ClusterTree.h:16: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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); | ^ 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, | ^~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp:998:9: note: 'n' was declared here 998 | int n, llimit, ulimit; | ^ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -dM -E -o moc_predefs.h /usr/lib/aarch64-linux-gnu/qt5/mkspecs/features/data/dummy.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.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/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"); | ^~~~~~~~~~~~~~ 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"); | ^~~~~~~~~~~~~~ /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.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++/13/memory:78, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:10: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include FileDialog.h -o moc_FileDialog.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-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/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/general -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/alignment -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/fileInput -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/interface -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/pairwise -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree -I/build/reproducible-path/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/aarch64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/aarch64-linux-gnu/13/include -I/usr/local/include -I/usr/include/aarch64-linux-gnu -I/usr/include WritePostscriptFile.h -o moc_WritePostscriptFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp 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"); | ^~~~~~~~~~~~~~ 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++/13/memory:78, from moc_BootstrapTreeDialog.cpp:9: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ 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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-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"); | ^~~~~~~~~~~~~~ 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"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-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 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++/13/memory:78, from moc_AlignOutputFileNames.cpp:9: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/qt5 -I/usr/include/aarch64-linux-gnu/qt5/QtWidgets -I/usr/include/aarch64-linux-gnu/qt5/QtGui -I/usr/include/aarch64-linux-gnu/qt5/QtXml -I/usr/include/aarch64-linux-gnu/qt5/QtCore -I. -I/usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp 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"); | ^~~~~~~~~~~~~~ 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/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++/13/memory:78, from moc_mainwindow.cpp:9: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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 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++/13/memory:78, from moc_TreeOutputFileNames.cpp:9: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/memory:78, from moc_WritePostscriptFile.cpp:9: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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/aarch64-linux-gnu/libQt5Widgets.so /usr/lib/aarch64-linux-gnu/libQt5Gui.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so /usr/lib/aarch64-linux-gnu/libQt5Core.so -lGL -lpthread /usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./clustalW/multipleAlign/Iteration.cpp:231:(.text+0x10d4): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/clustalx-2.1+lgpl' dh_installchangelogs debian/CHANGELOG.upstream make[1]: Leaving directory '/build/reproducible-path/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' in '../clustalx_2.1+lgpl-9_arm64.deb'. dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-9_arm64.deb'. dpkg-genbuildinfo --build=binary -O../clustalx_2.1+lgpl-9_arm64.buildinfo dpkg-genchanges --build=binary -O../clustalx_2.1+lgpl-9_arm64.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/3072304/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3072304/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/3072304 and its subdirectories I: Current time: Wed May 8 05:07:51 +14 2024 I: pbuilder-time-stamp: 1715094471