I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 29 12:12:41 +14 2024 I: pbuilder-time-stamp: 1714342361 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/3399342/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 28 22:12 /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/3399342/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3399342/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]="x86_64-pc-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=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=775049f925bc48e4aa9dcd3932b06526 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3399342 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.kRO2LDTO/pbuilderrc_Uosy --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.kRO2LDTO/b2 --logfile b2/build.log clustalx_2.1+lgpl-9.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 22 13:10 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3399342/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), qtbase5-dev, qtbase5-dev-tools, qttools5-dev-tools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19900 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} libclang1-15{a} libcups2{a} libdbus-1-3{a} libdebhelper-perl{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} 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} 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} libllvm15{a} libllvm17{a} libmagic-mgc{a} libmagic1{a} libmd4c0{a} libmtdev1t64{a} libopengl-dev{a} libopengl0{a} liborc-0.4-0t64{a} libpciaccess0{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} libqt5concurrent5{a} libqt5core5a{a} libqt5dbus5{a} libqt5designer5{a} libqt5designercomponents5{a} libqt5gui5{a} libqt5help5{a} libqt5network5{a} libqt5positioning5{a} libqt5printsupport5{a} libqt5qml5{a} libqt5qmlmodels5{a} libqt5quick5{a} libqt5quickwidgets5{a} libqt5sensors5{a} libqt5sql5{a} libqt5sql5-sqlite{a} libqt5test5{a} libqt5webchannel5{a} libqt5webkit5{a} libqt5widgets5{a} libqt5xml5{a} 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 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, 194 newly installed, 0 to remove and 0 not upgraded. Need to get 153 MB of archives. After unpacking 681 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.78.4-7 [1455 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libdw1t64 amd64 0.191-1+b1 [246 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libunwind8 amd64 1.6.2-3+b1 [51.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libcap2-bin amd64 1:2.66-5 [34.8 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libgstreamer1.0-0 amd64 1.22.10-1 [1184 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 liborc-0.4-0t64 amd64 1:0.4.38-1 [191 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 iso-codes all 4.16.0-1 [2936 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libgstreamer-plugins-base1.0-0 amd64 1.22.10-1 [964 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libhyphen0 amd64 2.8.8-7+b1 [30.6 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-1 [751 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdouble-conversion3 amd64 3.3.0-1+b1 [41.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libqt5core5a amd64 5.15.10+dfsg-7 [1834 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 28 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 23.3.5-1 [40.3 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 23.3.5-1 [35.8 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 48 http://deb.debian.org/debian trixie/main amd64 libegl-mesa0 amd64 23.3.5-1 [118 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libegl1 amd64 1.7.0-1+b1 [34.3 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libllvm17 amd64 1:17.0.6-5 [23.7 MB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 23.3.5-1 [8145 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 23.3.5-1 [150 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libevdev2 amd64 1.13.1+dfsg-1+b1 [32.6 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libmtdev1t64 amd64 1.1.6-1.2 [22.2 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libgudev-1.0-0 amd64 238-3 [14.3 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libwacom-common all 2.10.0-1 [62.4 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libwacom9 amd64 2.10.0-1 [22.4 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libinput-bin amd64 1.25.0-1 [24.6 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libinput10 amd64 1.25.0-1 [128 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libmd4c0 amd64 0.4.8-1+b1 [45.1 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libqt5dbus5 amd64 5.15.10+dfsg-7 [213 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libqt5network5 amd64 5.15.10+dfsg-7 [676 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libxcb-icccm4 amd64 0.4.1-1.1+b1 [26.8 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libxcb-image0 amd64 0.4.0-2+b1 [22.2 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libxcb-shape0 amd64 1.15-1 [106 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libxcb-xinerama0 amd64 1.15-1 [105 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libxcb-xinput0 amd64 1.15-1 [130 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxcb-xkb1 amd64 1.15-1 [129 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.41-2 [795 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libxkbcommon-x11-0 amd64 1.6.0-1+b1 [16.2 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libqt5gui5 amd64 5.15.10+dfsg-7 [3442 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libqt5positioning5 amd64 5.15.10+dfsg-3+b1 [206 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-13+b1 [111 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-13+b1 [43.3 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-13+b1 [47.1 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libcups2 amd64 2.4.7-1+b1 [247 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libqt5widgets5 amd64 5.15.10+dfsg-7 [2385 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libqt5printsupport5 amd64 5.15.10+dfsg-7 [203 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libqt5qml5 amd64 5.15.10+dfsg-2+b1 [1361 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libqt5qmlmodels5 amd64 5.15.10+dfsg-2+b1 [191 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libqt5quick5 amd64 5.15.10+dfsg-2+b1 [1596 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libqt5sensors5 amd64 5.15.10-2+b1 [113 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libqt5webchannel5 amd64 5.15.10-2+b1 [58.6 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libwoff1 amd64 1.0.2-2+b1 [44.4 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libqt5webkit5 amd64 5.212.0~alpha4-33+b1 [11.9 MB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.8-1 [817 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.8-1 [2037 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.8-1 [1825 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.8-1 [597 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get: 129 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-2+b1 [314 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libmagic1 amd64 1:5.45-2+b1 [105 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-2+b1 [43.1 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 152 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libllvm15 amd64 1:15.0.7-10 [23.2 MB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libclang1-15 amd64 1:15.0.7-10 [6377 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.9-1+b1 [21.3 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.2-3+b1 [40.8 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libpthread-stubs0-dev amd64 0.4-1+b1 [5348 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.7-1+b1 [875 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libglx-dev amd64 1.7.0-1+b1 [15.8 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libgl-dev amd64 1.7.0-1+b1 [101 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libegl-dev amd64 1.7.0-1+b1 [19.5 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b1 [31.1 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b1 [180 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libopengl-dev amd64 1.7.0-1+b1 [5380 B] Get: 173 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b1 [219 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libqt5concurrent5 amd64 5.15.10+dfsg-7 [43.2 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libqt5xml5 amd64 5.15.10+dfsg-7 [123 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libqt5designer5 amd64 5.15.10-6 [2749 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libqt5designercomponents5 amd64 5.15.10-6 [730 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libqt5sql5 amd64 5.15.10+dfsg-7 [123 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libqt5help5 amd64 5.15.10-6 [149 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libqt5quickwidgets5 amd64 5.15.10+dfsg-2+b1 [40.0 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libqt5sql5-sqlite amd64 5.15.10+dfsg-7 [57.9 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libqt5test5 amd64 5.15.10+dfsg-7 [148 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libvulkan-dev amd64 1.3.280.0-1 [1348 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 qtchooser amd64 66-2 [26.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 qdoc-qt5 amd64 5.15.10-6 [589 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 qhelpgenerator-qt5 amd64 5.15.10-6 [58.2 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 qt5-assistant amd64 5.15.10-6 [350 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 qt5-qmake-bin amd64 5.15.10+dfsg-7 [1044 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 qt5-qmake amd64 5.15.10+dfsg-7 [222 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 qtattributionsscanner-qt5 amd64 5.15.10-6 [30.8 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 qtbase5-dev-tools amd64 5.15.10+dfsg-7 [761 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 qtbase5-dev amd64 5.15.10+dfsg-7 [1121 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 qttools5-dev-tools amd64 5.15.10-6 [1033 kB] Fetched 153 MB in 13s (12.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libglib2.0-0t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19900 files and directories currently installed.) Preparing to unpack .../000-libglib2.0-0t64_2.78.4-7_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.78.4-7) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../001-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package libdw1t64:amd64. Preparing to unpack .../002-libdw1t64_0.191-1+b1_amd64.deb ... Unpacking libdw1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package libunwind8:amd64. Preparing to unpack .../003-libunwind8_1.6.2-3+b1_amd64.deb ... Unpacking libunwind8:amd64 (1.6.2-3+b1) ... Selecting previously unselected package libcap2-bin. Preparing to unpack .../004-libcap2-bin_1%3a2.66-5_amd64.deb ... Unpacking libcap2-bin (1:2.66-5) ... Selecting previously unselected package libgstreamer1.0-0:amd64. Preparing to unpack .../005-libgstreamer1.0-0_1.22.10-1_amd64.deb ... Unpacking libgstreamer1.0-0:amd64 (1.22.10-1) ... Selecting previously unselected package liborc-0.4-0t64:amd64. Preparing to unpack .../006-liborc-0.4-0t64_1%3a0.4.38-1_amd64.deb ... Unpacking liborc-0.4-0t64:amd64 (1:0.4.38-1) ... Selecting previously unselected package iso-codes. Preparing to unpack .../007-iso-codes_4.16.0-1_all.deb ... Unpacking iso-codes (4.16.0-1) ... Selecting previously unselected package libgstreamer-plugins-base1.0-0:amd64. Preparing to unpack .../008-libgstreamer-plugins-base1.0-0_1.22.10-1_amd64.deb ... Unpacking libgstreamer-plugins-base1.0-0:amd64 (1.22.10-1) ... Selecting previously unselected package libhyphen0:amd64. Preparing to unpack .../009-libhyphen0_2.8.8-7+b1_amd64.deb ... Unpacking libhyphen0:amd64 (2.8.8-7+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../010-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../011-libjpeg62-turbo_1%3a2.1.5-2+b2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../012-libpng16-16t64_1.6.43-5_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../013-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../014-shared-mime-info_2.4-1_amd64.deb ... Unpacking shared-mime-info (2.4-1) ... Selecting previously unselected package libdouble-conversion3:amd64. Preparing to unpack .../015-libdouble-conversion3_3.3.0-1+b1_amd64.deb ... Unpacking libdouble-conversion3:amd64 (3.3.0-1+b1) ... Selecting previously unselected package libpcre2-16-0:amd64. Preparing to unpack .../016-libpcre2-16-0_10.42-4+b1_amd64.deb ... Unpacking libpcre2-16-0:amd64 (10.42-4+b1) ... Selecting previously unselected package libqt5core5a:amd64. Preparing to unpack .../017-libqt5core5a_5.15.10+dfsg-7_amd64.deb ... Unpacking libqt5core5a:amd64 (5.15.10+dfsg-7) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../018-libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../019-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../020-libfreetype6_2.13.2+dfsg-1+b4_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../021-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 .../022-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../023-fontconfig-config_2.15.0-1.1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../024-libfontconfig1_2.15.0-1.1_amd64.deb ... 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Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libllvm15:amd64 (1:15.0.7-10) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libqt5sensors5:amd64 (5.15.10-2+b1) ... Setting up libqt5test5:amd64 (5.15.10+dfsg-7) ... Setting up libllvm17:amd64 (1:17.0.6-5) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libqt5concurrent5:amd64 (5.15.10+dfsg-7) ... Setting up libavahi-client3:amd64 (0.8-13+b1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libinput10:amd64 (1.25.0-1) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libgbm1:amd64 (23.3.5-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-1) ... Setting up libqt5positioning5:amd64 (5.15.10+dfsg-3+b1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (23.3.5-1) ... Setting up libx11-dev:amd64 (2:1.8.7-1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libclang1-15 (1:15.0.7-10) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libqt5network5:amd64 (5.15.10+dfsg-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libqt5sql5:amd64 (5.15.10+dfsg-7) ... Setting up qtbase5-dev-tools (5.15.10+dfsg-7) ... Setting up libqt5xml5:amd64 (5.15.10+dfsg-7) ... Setting up libegl-mesa0:amd64 (23.3.5-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libqt5qml5:amd64 (5.15.10+dfsg-2+b1) ... Setting up qtattributionsscanner-qt5 (5.15.10-6) ... Setting up libqt5webchannel5:amd64 (5.15.10-2+b1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b1) ... Setting up libcups2:amd64 (2.4.7-1+b1) ... Setting up libegl1:amd64 (1.7.0-1+b1) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libqt5qmlmodels5:amd64 (5.15.10+dfsg-2+b1) ... Setting up libglx-mesa0:amd64 (23.3.5-1) ... Setting up libqt5sql5-sqlite:amd64 (5.15.10+dfsg-7) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up qdoc-qt5 (5.15.10-6) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up libglx-dev:amd64 (1.7.0-1+b1) ... Setting up libgl-dev:amd64 (1.7.0-1+b1) ... Setting up libvulkan-dev:amd64 (1.3.280.0-1) ... Setting up libegl-dev:amd64 (1.7.0-1+b1) ... Setting up libqt5gui5:amd64 (5.15.10+dfsg-7) ... Setting up libqt5widgets5:amd64 (5.15.10+dfsg-7) ... Setting up libqt5help5:amd64 (5.15.10-6) ... Setting up libqt5printsupport5:amd64 (5.15.10+dfsg-7) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b1) ... Setting up qtbase5-dev:amd64 (5.15.10+dfsg-7) ... Setting up libqt5quick5:amd64 (5.15.10+dfsg-2+b1) ... Setting up libqt5designer5:amd64 (5.15.10-6) ... Setting up qhelpgenerator-qt5 (5.15.10-6) ... Setting up libqt5webkit5:amd64 (5.212.0~alpha4-33+b1) ... Setting up libqt5designercomponents5:amd64 (5.15.10-6) ... Setting up libqt5quickwidgets5:amd64 (5.15.10+dfsg-2+b1) ... Setting up qt5-assistant (5.15.10-6) ... Setting up qttools5-dev-tools (5.15.10-6) ... Processing triggers for libc-bin (2.37-18) ... 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/3399342/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3399342/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 amd64 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection:" \ -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 -fcf-protection:" \ -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 -j20 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentWidget.o AlignmentWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignOutputFileNames.o AlignOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColorFileXmlParser.o ColorFileXmlParser.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] 74 | // tr("colorrules not found in the parameter file, using\ | ^ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp 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"); | ^~~~~~~~~~~~~~ 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"); | ^~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'QColor ColorParameters::getResidueColor(QChar, QChar)': ColorParameters.cpp:160:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 160 | for(i = 0; i < colorPar.size(); i++) | ~~^~~~~~~~~~~~~~~~~ ColorParameters.cpp:174:26: warning: unused variable 'temp' [-Wunused-variable] 174 | char temp = colorPar[i].consensusConditionList[j].toLatin1(); | ^~~~ ColorParameters.cpp:157:10: warning: unused variable 'showRes' [-Wunused-variable] 157 | char showRes = res.toLatin1(); | ^~~~~~~ ColorParameters.cpp:158:10: warning: unused variable 'showCon' [-Wunused-variable] 158 | char showCon = consensus.toLatin1(); | ^~~~~~~ ColorParameters.cpp: In member function 'int ColorParameters::getResidueColorNum(QChar, QChar)': ColorParameters.cpp:197:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 197 | for(i = 0; i < colorPar.size(); i++) | ~~^~~~~~~~~~~~~~~~~ ColorParameters.cpp:211:26: warning: unused variable 'temp' [-Wunused-variable] 211 | char temp = colorPar[i].consensusConditionList[j].toLatin1(); | ^~~~ ColorParameters.cpp:194:10: warning: unused variable 'showRes' [-Wunused-variable] 194 | char showRes = res.toLatin1(); | ^~~~~~~ ColorParameters.cpp:195:10: warning: unused variable 'showCon' [-Wunused-variable] 195 | char showCon = consensus.toLatin1(); | ^~~~~~~ ColorParameters.cpp: In member function 'void ColorParameters::printColorInfo()': ColorParameters.cpp:229:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 229 | for(int i = 0; i < colors.size(); i++) | ~~^~~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'int ColorParameters::getIndexOfColor(QColor)': ColorParameters.cpp:238:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 238 | for(int i = 0; i < colors.size(); i++) | ~~^~~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'QColor ColorParameters::getColorFromNum(int)': ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 251 | if(colorNum > 0 && colorNum - 1 < colorPar.size()) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 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"); | ^~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from HardCodedColorScheme.cpp:1: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp 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/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qbrush.h:52, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpalette.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qwidget.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QWidget:1, from QTUtility.h:10, from main.cpp:22: /usr/include/c++/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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp 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"); | ^~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp 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/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from BootstrapTreeDialog.cpp:8: /usr/include/c++/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 HardCodedColorScheme.h:8, from ColorParameters.h:11, from ColorFileXmlParser.h:9, from ColorFileXmlParser.cpp:3: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from 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"); | ^~~~~~~~~~~~~~ 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 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/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdebug.h:54, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborcommon.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborvalue.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborarray.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:38, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from AlignmentViewerWidget.cpp:63: /usr/include/c++/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 AlignOutputFileNames.h:10, from AlignOutputFileNames.cpp:26: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 106 | auto_ptr outFileNames; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from AlignOutputFileNames.cpp:16: /usr/include/c++/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 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) | ~~~~~~~~~~~~^~~~~ 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/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdebug.h:54, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborcommon.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborvalue.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qcborarray.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:38, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:3, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from mainwindow.cpp:90: /usr/include/c++/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) | ~~~~^~~~ In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from PairwiseParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ PairwiseParams.cpp: In member function 'virtual void PairwiseParams::showEvent(QShowEvent*)': PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] 74 | void PairwiseParams::showEvent(QShowEvent* event) | ~~~~~~~~~~~~^~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)': HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 180 | if(column >= 0 && column < arrayOfHeights->size()) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 198 | if(column >= 0 && column < arrayOfHeights->size()) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ HistogramWidget.cpp:208:47: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 208 | (fontMetrics.width(QString::number(rulerNum))) / 2; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qwidget.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qframe.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qlabel.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QLabel:1, from HistogramWidget.h:29, from HistogramWidget.cpp:23: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ HistogramWidget.cpp:241:61: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 241 | (fontMetrics.width(QString::number(0))) / 2, yPos, boxWidth, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp 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"); | ^~~~~~~~~~~~~~ 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"); | ^~~~~~~~~~~~~~ AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)': AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder] 170 | bool blackAndWhite; | ^~~~~~~~~~~~~ AlignmentWidget.h:161:27: warning: 'std::vector >* AlignmentWidget::selectedColoredRes' [-Wreorder] 161 | std::vector* selectedColoredRes; | ^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] 65 | AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) | ^~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calculatePixMaps()': AlignmentWidget.cpp:225:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 225 | for(unsigned int j = 0; j < lengthLongestSeq; j++) | ~~^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:235:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 235 | if(code >= 0 && code < conservationPixmaps->size()) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:268:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 268 | if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:280:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 280 | if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:291:86: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 291 | if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j) | ~~~~~~~~~~~~~~~~~~~~~^~~ AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable] 215 | int codeForSpace = clustalw::userParameters->resIndex( | ^~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::generateSecStructurePixmaps()': AlignmentWidget.cpp:333:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 333 | if(i < secStructPixmaps->size() && i < secStructInfo.size()) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:344:34: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 344 | fontMetrics.width(secStructInfo[i])/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QtGui:26, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from AlignmentWidget.cpp:48: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::drawContents(QPainter*, int, int, int, int)': AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 569 | if(selectedRes >= selectedColoredRes->size()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) | ~~~~~~~~~~~~~~~~~^~~~~ 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())) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) | ~~~~~~~~~~~~~~~~~^~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~ 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 | ^~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::makeColorMask(clustalw::Array2D*, ColorParameters*)': AlignmentWidget.cpp:878:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 878 | if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()': AlignmentWidget.cpp:927:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 927 | if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()': AlignmentWidget.cpp:1039:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1039 | for(int j = 0; j < aminoAcid.size(); j++) | ~~^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:1051:49: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1051 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp:1079:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1079 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp:1089:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1089 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp:1099:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1099 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ AlignmentWidget.cpp:1118:30: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1118 | fontMetrics.width(currentChar)/2, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ 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/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"); | ^~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~ 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) | ~~~~~~~~~~~~^~~~~ 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/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; | ^~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp 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; | ^~~~~~~~ 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; | ^~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from 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/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from SaveSeqFile.cpp:14: /usr/include/c++/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 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"); | ^~~~~~~~~~~~~~ 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/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 */ | ^~ 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: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/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/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) | ^ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp 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/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(); | ^~~~~~~~~~ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1156:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 1156 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1445:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 1445 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1560:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 1560 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:2095:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 2095 | catch(VectorOutOfRange e) | ^ clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 2102 | catch(exception e) | ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)': clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] 2351 | catch(VectorOutOfRange e) | ^ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp 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"); | ^~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp 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; | ^ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from SeqNameWidget.cpp:59: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)': SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable] 375 | QRect redrawRect = event->rect(); | ^~~~~~~~~~ SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()': SeqNameWidget.cpp:443:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 443 | int length = fontMetrics.width(QString(name.c_str())); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QtGui:26, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QtWidgets:3, from SeqNameWidget.cpp:58: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp 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) | ~~~~^~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp clustalW/fileInput/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, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp 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) | ~~~~~^~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp clustalW/general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)': clustalW/general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 475 | register int i; | ^ clustalW/general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)': clustalW/general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 53 | register int p; | ^ clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)': clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable] 251 | int n; | ^ clustalW/general/Utility.cpp: In member function 'virtual void clustalw::Utility::setInfoLabelPtr(QLabel*)': clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] 519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) | ~~~~~~~~^~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp 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/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from WritePostscriptFile.cpp:14: /usr/include/c++/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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp In file included from 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; | ^~~~~~~~ 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/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/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/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/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"); | ^~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp 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/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; | ^~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp In file included from clustalW/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/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 231 | tmpnam (buffer); | ~~~~~~~^~~~~~~~ In file included from clustalW/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; | ^~~~~~~~ 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"); | ^~~~~~~~~~~~~~ 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"); | ^~~~~~~~~~~~~~ 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/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"); | ^~~~~~~~~~~~~~ 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; | ^~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileWithSub.h:9, from clustalW/multipleAlign/ProfileWithSub.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/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"); | ^~~~~~~~~~~~~~ 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/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/x86_64-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmap.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qicon.h:46, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qpushbutton.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPushButton:1, from TreeOutputFileNames.cpp:7: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()': clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] 520 | clustalObj->getHelp('C'); | ~~~~~~~~~~~~~~~~~~~^~~~~ clustalW/interface/InteractiveMenu.cpp:521:13: note: here 521 | case 'Q': | ^~~~ clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1190 | system(lin1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, from clustalW/pairwise/FullPairwiseAlign.h:9, from clustalW/pairwise/FullPairwiseAlign.cpp:9: clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, from clustalW/pairwise/FastPairwiseAlign.h:9, from clustalW/pairwise/FastPairwiseAlign.cpp:10: clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::tempInterface(int, int)': clustalW/substitutionMatrix/SubMatrix.cpp:1613:35: warning: unused parameter 'alignResidueType' [-Wunused-parameter] 1613 | void SubMatrix::tempInterface(int alignResidueType, int alignType) | ~~~~^~~~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp:1613:57: warning: unused parameter 'alignType' [-Wunused-parameter] 1613 | void SubMatrix::tempInterface(int alignResidueType, int alignType) | ~~~~^~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])': clustalW/substitutionMatrix/SubMatrix.cpp:1657:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] 1657 | int maxRes; | ^~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])': clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] 1717 | int maxRes; | ^~~~~~ g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp 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"); | ^~~~~~~~~~~~~~ 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; | ^~~~~~~~ In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11: clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ /usr/include/c++/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; | ^~~~~~~~ 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"); | ^~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp clustalW/tree/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; | ^~~~~~~~ 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"); | ^~~~~~~~~~~~~~ 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; | ^~~~~~~~ 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; | ^ g++ -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -dM -E -o moc_predefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/features/data/dummy.cpp /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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.cpp In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/TreeInterface.h:19, from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ 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/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/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; | ^~~~~~~~ /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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include ColumnScoreParams.h -o moc_ColumnScoreParams.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/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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include HistogramWidget.h -o moc_HistogramWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include LowScoringSegParams.h -o moc_LowScoringSegParams.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include mainwindow.h -o moc_mainwindow.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include ProteinGapParameters.h -o moc_ProteinGapParameters.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include PSPrinter.h -o moc_PSPrinter.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include SearchForString.h -o moc_SearchForString.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/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include SecStructOptions.h -o moc_SecStructOptions.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include SeqNameWidget.h -o moc_SeqNameWidget.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include TreeFormatOptions.h -o moc_TreeFormatOptions.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/reproducible-path/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/x86_64-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/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13 -I/usr/include/c++/13/backward -I/usr/lib/gcc/x86_64-linux-gnu/13/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include WritePostscriptFile.h -o moc_WritePostscriptFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)': clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized] 1103 | return (maxRes); | ^ clustalW/substitutionMatrix/SubMatrix.cpp:998:9: note: 'n' was declared here 998 | int n, llimit, ulimit; | ^ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from 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"); | ^~~~~~~~~~~~~~ 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; | ^~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from BootstrapTreeDialog.h:11, from moc_BootstrapTreeDialog.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from 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"); | ^~~~~~~~~~~~~~ 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; | ^~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp 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"); | ^~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp g++ -c -pipe -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalx-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from ColorFileXmlParser.h:9, from moc_ColorFileXmlParser.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from 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 SaveSeqFile.h:9, from moc_SaveSeqFile.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from 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/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 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; | ^~~~~~~~ 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; | ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o /usr/lib/x86_64-linux-gnu/libQt5Widgets.so /usr/lib/x86_64-linux-gnu/libQt5Gui.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so /usr/lib/x86_64-linux-gnu/libQt5Core.so -lGL -lpthread /usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./clustalW/multipleAlign/Iteration.cpp:231:(.text+0x10e0): 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_amd64.deb'. dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../clustalx_2.1+lgpl-9_amd64.buildinfo dpkg-genchanges --build=binary -O../clustalx_2.1+lgpl-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3399342/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3399342/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/3399342 and its subdirectories I: Current time: Mon Apr 29 12:17:21 +14 2024 I: pbuilder-time-stamp: 1714342641