Thu Sep 4 11:47:11 UTC 2025 I: starting to build clustalw/forky/arm64 on jenkins on '2025-09-04 11:46' Thu Sep 4 11:47:11 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/95535/console.log Thu Sep 4 11:47:11 UTC 2025 I: Downloading source for forky/clustalw=2.1+lgpl-7 --2025-09-04 11:47:11-- http://deb.debian.org/debian/pool/main/c/clustalw/clustalw_2.1%2blgpl-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2055 (2.0K) [text/prs.lines.tag] Saving to: ‘clustalw_2.1+lgpl-7.dsc’ 0K .. 100% 245M=0s 2025-09-04 11:47:11 (245 MB/s) - ‘clustalw_2.1+lgpl-7.dsc’ saved [2055/2055] Thu Sep 4 11:47:11 UTC 2025 I: clustalw_2.1+lgpl-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: clustalw Binary: clustalw Architecture: any Version: 2.1+lgpl-7 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: http://www.clustal.org/clustal2/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/clustalw Vcs-Git: https://salsa.debian.org/med-team/clustalw.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: clustalw deb science optional arch=any Checksums-Sha1: f29784f68585544baa77cbeca6392e533d4cf433 350761 clustalw_2.1+lgpl.orig.tar.gz ca05ae4a01ee2f310674eb3ad0f13bdbd5687f70 20292 clustalw_2.1+lgpl-7.debian.tar.xz Checksums-Sha256: e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486 350761 clustalw_2.1+lgpl.orig.tar.gz ba8006f86ea11234e17d0a1fa97d3e31ecfc075ba42c9840b45a15468cb3abfa 20292 clustalw_2.1+lgpl-7.debian.tar.xz Files: 144df8440a0ae083d5167616c8ceeb41 350761 clustalw_2.1+lgpl.orig.tar.gz ff53dd21d7d2e701119fc09dd6373a0f 20292 clustalw_2.1+lgpl-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+yO6kRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF/lg//UKZUVJVxdXv2F2zS19v/O0w3yAxkiHZ/ PZsLldjC0zPHGm8bGV+OBwf7WncslvQRWCJRUs5N8eKnYPmUP8lQARt/IVBVgjYs 750k+sMiw/MJMHBou7tm+dDhSlCB/3ifn0dR214f9arPh2KMwQXse/PSCcqOrXlb EoGvRte6lfbXJQ3i8lHzGMg3JrgwQyPffRItNbeoIRyw/vyJO+mRpUaOW6IJKPFg WHBqekaBgyoDzrHjMeTlIOBNipqsRa/MAgr0hFBD8pymwS5byVXIPfnZyStpnoMT DD9jqGFWYkAiGooMFwN0OF3XLsDXSNlRcDfwwCnAHIuzxYJm5pbLudpDTNr78a6M ikWmqaYhR6vBj4ta9XlnUOfkVp8C5SCV0wZ9JdAKvUhkHYmoe6fZa4vgH40NK57q y0qqwpn7qufghZrY/jr6KjC63G225koyJKH2qgbR8p1/aiQ6If7ZuRXR84bD9vOW YYt6hdni7l10ploT2u6NL44qsM2GJFkyaqYY6gvtvYy7eCmUECbotSoClrILAuxw u4ATxvnzoLNMd9YC/cuRQXcpQeMGDkFGU8sbFmJMYFbJeBIKNZE4cGmgcTg77BLR k7pjFYpytX5PYAKDfergKaauiO8mpa3368bACSQTf43x8jR9tW5WfDfMJL+UogVf kdKCxiIYjko= =4+ai -----END PGP SIGNATURE----- Thu Sep 4 11:47:11 UTC 2025 I: Checking whether the package is not for us Thu Sep 4 11:47:11 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Thu Sep 4 11:47:11 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Thu Sep 4 11:47:55 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 7 06:10:12 -12 2026 I: pbuilder-time-stamp: 1791396612 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [clustalw_2.1+lgpl-7.dsc] I: copying [./clustalw_2.1+lgpl.orig.tar.gz] I: copying [./clustalw_2.1+lgpl-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./clustalw_2.1+lgpl-7.dsc: no acceptable signature found dpkg-source: info: extracting clustalw in clustalw-2.1+lgpl dpkg-source: info: unpacking clustalw_2.1+lgpl.orig.tar.gz dpkg-source: info: unpacking clustalw_2.1+lgpl-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/362812/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='edba8e21bdd246ab90de6d0c8c950a31' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='362812' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QCIXB25x/pbuilderrc_2Jah --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QCIXB25x/b1 --logfile b1/build.log clustalw_2.1+lgpl-7.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/362812/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20011 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. 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} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After unpacking 44.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.1-1 [93.8 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-1 [316 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.14.2-1 [19.8 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.14.2-1 [8768 B] Get: 22 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.2 [582 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 debhelper all 13.26 [939 kB] Fetched 11.0 MB in 0s (138 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 20011 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-1_arm64.deb ... Unpacking bsdextrautils (2.41.1-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_arm64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.2-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_arm64.deb ... Unpacking libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.2-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.2-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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: Running cd /build/reproducible-path/clustalw-2.1+lgpl/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../clustalw_2.1+lgpl-7_source.changes dpkg-buildpackage: info: source package clustalw dpkg-buildpackage: info: source version 2.1+lgpl-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:40: warning: The macro 'AC_CANONICAL_SYSTEM' is obsolete. configure.ac:40: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:40: the top level configure.ac:90: warning: The macro 'AC_LANG_CPLUSPLUS' is obsolete. configure.ac:90: You should run autoupdate. ./lib/autoconf/c.m4:270: AC_LANG_CPLUSPLUS is expanded from... configure.ac:90: the top level configure.ac:94: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:94: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:94: the top level configure.ac:111: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:111: You should use the 'AC_CONFIG_HEADERS' macro instead. aclocal.m4:707: AM_CONFIG_HEADER is expanded from... configure.ac:111: the top level configure.ac:133: warning: AC_OUTPUT should be used without arguments. configure.ac:133: You should run autoupdate. configure.ac:79: installing './compile' src/Makefile.am:21: warning: source file './pairwise/FullPairwiseAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibility. src/Makefile.am:21: warning: source file './pairwise/FastPairwiseAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/MSFFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/FileReader.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/PIRFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/RSFFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/GDEFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/InFileStream.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/ClustalFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/PearsonFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/FileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/EMBLFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/UPGMAAlgorithm.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/Node.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedGuideTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedTreeOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/Tree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/ClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/TreeInterface.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UnRootedClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/ClusterTreeOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/RandomGenerator.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/NJTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/AlignmentSteps.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './interface/InteractiveMenu.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './interface/CommandLineParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './substitutionMatrix/SubMatrix.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/Iteration.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/MSA.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/MyersMillerProfileAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileStandard.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileWithSub.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileBase.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/LowScoreSegProfile.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/OutputFile.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/UserParameters.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/Utility.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/InvalidCombination.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/DebugLog.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/ClustalWResources.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/VectorOutOfRange.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/SymMatrix.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/Stats.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './Help.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/Alignment.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/AlignmentOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/ObjectiveScore.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/Sequence.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './Clustal.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './main.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking target system type... aarch64-unknown-linux-gnu building for linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether make sets $(MAKE)... (cached) yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for _Bool... no checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for GNU libc compatible malloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' Making all in m4 make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/m4' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/m4' Making all in src make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make all-recursive make[3]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[4]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/src' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp ./fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()': ./fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 37 | register int i; | ^ ./fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 38 | register char c; | ^ In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./fileInput/FileReader.cpp:29: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FullPairwiseAlign.h:9, from ./pairwise/FullPairwiseAlign.cpp:9: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./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++/14/memory:78, from ./fileInput/FileReader.h:11: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./fileInput/FileReader.cpp: At global scope: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FastPairwiseAlign.h:9, from ./pairwise/FastPairwiseAlign.cpp:10: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/../ClusterTree.h:20, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/UPGMA/../ClusterTree.h:23: ./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++/14/memory:78, from ./tree/UPGMA/../ClusterTree.h:16: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/UPGMA/RootedClusterTree.cpp: In member function 'std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/UPGMAAlgorithm.h:8, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./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++/14/memory:78, from ./tree/UPGMA/UPGMAAlgorithm.h:10: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedGuideTree.cpp:10: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedTreeOutput.h:15, from ./tree/UPGMA/RootedTreeOutput.cpp:9: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, from ./tree/ClusterTree.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp In file included from ./tree/ClusterTree.h:23: ./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++/14/memory:78, from ./tree/ClusterTree.h:16: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/memory:78, from ./tree/Tree.h:15: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/Tree.cpp: In member function 'std::auto_ptr clustalw::Tree::createSets(int, int)': ./tree/Tree.cpp:280:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 280 | auto_ptr progAlignSteps; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/ClusterTree.h:23: ./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++/14/memory:78, from ./tree/ClusterTree.h:16: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/TreeInterface.h:19, from ./tree/TreeInterface.cpp:15: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./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++/14/memory:78, from ./tree/TreeInterface.h:17: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/ClusterTree.h:23, from ./tree/UnRootedClusterTree.h:8, from ./tree/TreeInterface.cpp:17: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:18: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:23: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::string*, std::vector*, int, int, bool*)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::string*, std::vector*, int, int, bool*)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTreeOutput.h:11, from ./tree/ClusterTreeOutput.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, from ./interface/../Clustal.h:18, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./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++/14/memory:78, from ./interface/../fileInput/FileReader.h:11: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)': ./tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 164 | register int i; | ^ In file included from ./substitutionMatrix/SubMatrix.cpp:15: ./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"); | ^~~~~~~~~~~~~~ ./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 ./multipleAlign/Iteration.cpp:17: ./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++/14/memory:78, from ./multipleAlign/../tree/TreeInterface.h:17: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, from ./interface/../Clustal.h:18, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./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++/14/memory:78, from ./interface/../fileInput/FileReader.h:11: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': ./interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1190 | system(lin1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp ./multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 231 | tmpnam (buffer); | ~~~~~~~^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/MSA.h:10, from ./multipleAlign/MSA.cpp:16: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileAlignAlgorithm.h:10, from ./multipleAlign/MyersMillerProfileAlign.h:10, from ./multipleAlign/MyersMillerProfileAlign.cpp:10: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileStandard.h:9, from ./multipleAlign/ProfileStandard.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileWithSub.h:9, from ./multipleAlign/ProfileWithSub.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/ProfileBase.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/LowScoreSegProfile.h:13, from ./multipleAlign/LowScoreSegProfile.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp In file included from ./general/OutputFile.cpp:9: ./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++/14/memory:78, from ./general/OutputFile.h:8: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp ./general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)': ./general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 475 | register int i; | ^ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp ./general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)': ./general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 53 | register int p; | ^ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp ./general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)': ./general/Utility.cpp:183:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ ./general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)': ./general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp In file included from ./general/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./general/../alignment/Alignment.h:42, from ./general/Stats.cpp:15: ./general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/ObjectiveScore.h:15, from ./alignment/ObjectiveScore.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./alignment/AlignmentOutput.h:24, from ./alignment/AlignmentOutput.cpp:27: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./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++/14/memory:78, from ./alignment/AlignmentOutput.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./alignment/Alignment.cpp:25: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()': ./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 */ | ^~ ./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()': ./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 */ | ^~ ./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()': ./alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 617 | register int sl; | ^~ In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./Clustal.h:18, from ./Clustal.cpp:27: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./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++/14/memory:78, from ./fileInput/FileReader.h:11: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./main.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./Clustal.cpp: In member function 'void clustalw::Clustal::align(std::string*, bool)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./Clustal.cpp: In member function 'void clustalw::Clustal::doAlignUseOldTree(std::string*)': ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./main.cpp:16: ./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++/14/memory:78, from ./fileInput/FileReader.h:11: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalw-2.1+lgpl=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o clustalw2 FullPairwiseAlign.o FastPairwiseAlign.o MSFFileParser.o FileReader.o PIRFileParser.o RSFFileParser.o GDEFileParser.o InFileStream.o ClustalFileParser.o PearsonFileParser.o FileParser.o EMBLFileParser.o RootedClusterTree.o UPGMAAlgorithm.o Node.o RootedGuideTree.o RootedTreeOutput.o Tree.o ClusterTree.o TreeInterface.o UnRootedClusterTree.o ClusterTreeOutput.o RandomGenerator.o NJTree.o AlignmentSteps.o InteractiveMenu.o CommandLineParser.o SubMatrix.o Iteration.o MSA.o MyersMillerProfileAlign.o ProfileStandard.o ProfileWithSub.o ProfileBase.o LowScoreSegProfile.o OutputFile.o UserParameters.o Utility.o InvalidCombination.o DebugLog.o ClustalWResources.o VectorOutOfRange.o SymMatrix.o Stats.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o Clustal.o main.o /usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./src/./multipleAlign/Iteration.cpp:231:(.text+0x10b8): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[4]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' make[1]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' Making check in m4 make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/m4' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/m4' Making check in src make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[3]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' make[1]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/clustalw/ make -j12 install DESTDIR=/build/reproducible-path/clustalw-2.1\+lgpl/debian/clustalw AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' Making install in m4 make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/m4' make[3]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/m4' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/m4' make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/m4' Making install in src make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[3]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[4]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/clustalw-2.1+lgpl/debian/clustalw/usr/bin' /usr/bin/install -c clustalw2 '/build/reproducible-path/clustalw-2.1+lgpl/debian/clustalw/usr/bin' make[4]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[3]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl/src' make[2]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' make[3]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' make[2]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' make[1]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' dh_install # We have to ask upstream if it is important for them that the binary is named clustalw2 mv /build/reproducible-path/clustalw-2.1+lgpl/debian/clustalw/usr/bin/clustalw2 /build/reproducible-path/clustalw-2.1+lgpl/debian/clustalw/usr/bin/clustalw make[1]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/clustalw-2.1+lgpl' dh_installchangelogs debian/CHANGELOG.upstream make[1]: Leaving directory '/build/reproducible-path/clustalw-2.1+lgpl' dh_installexamples dh_installman dh_installmenu 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'clustalw' in '../clustalw_2.1+lgpl-7_arm64.deb'. dpkg-deb: building package 'clustalw-dbgsym' in '../clustalw-dbgsym_2.1+lgpl-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../clustalw_2.1+lgpl-7_arm64.buildinfo dpkg-genchanges --build=binary -O../clustalw_2.1+lgpl-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/362812 and its subdirectories I: Current time: Wed Oct 7 06:10:54 -12 2026 I: pbuilder-time-stamp: 1791396654 Thu Sep 4 11:47:55 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Thu Sep 4 11:47:55 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Thu Sep 4 11:48:48 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Thu Sep 4 11:48:49 UTC 2025 I: clustalw_2.1+lgpl-7_arm64.changes: Format: 1.8 Date: Mon, 16 Nov 2020 09:33:34 +0100 Source: clustalw Binary: clustalw clustalw-dbgsym Architecture: arm64 Version: 2.1+lgpl-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: clustalw - global multiple nucleotide or peptide sequence alignment Changes: clustalw (2.1+lgpl-7) unstable; urgency=medium . [ Jelmer Vernooij ] * Use secure copyright file specification URI. * Trim trailing whitespace. . [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Set field Upstream-Contact in debian/copyright. * Remove obsolete field Contact from debian/upstream/metadata (already present in machine-readable debian/copyright). * watch file standard 4 (routine-update) Checksums-Sha1: 8b7e38bd8e6a2801897d1e7074f1a9b12f6d16ef 3733140 clustalw-dbgsym_2.1+lgpl-7_arm64.deb 855f195b0b41e9a5ae69aa5da0a3b568316350fb 4901 clustalw_2.1+lgpl-7_arm64.buildinfo 29eda1cb02bdf3cec41fb99caf72e4aeefd8518f 254820 clustalw_2.1+lgpl-7_arm64.deb Checksums-Sha256: 1dcd1b8031ce2455262f128b78bfb1222d5d436d3434ee4ff736a74ef97deede 3733140 clustalw-dbgsym_2.1+lgpl-7_arm64.deb 60ffbaf558f9d192cc3a3b2318ad7df147c74e81980a1e444498b4727c88b368 4901 clustalw_2.1+lgpl-7_arm64.buildinfo c4be084b47115c3027ee47c569174964ea97168a453f498d9d9fa6ce10bc05c2 254820 clustalw_2.1+lgpl-7_arm64.deb Files: 169745d62c29f23c69718648ad3fd379 3733140 debug optional clustalw-dbgsym_2.1+lgpl-7_arm64.deb c7fbb6df604ab0c67da330352097a836 4901 science optional clustalw_2.1+lgpl-7_arm64.buildinfo b811a2e0a2670cc20b6d0b2a1fda10e7 254820 science optional clustalw_2.1+lgpl-7_arm64.deb Thu Sep 4 11:48:49 UTC 2025 I: diffoscope 305 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_4-95535.service; invocation ID: dfc8dfa838e2462088f2351f36fbe4a9 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QCIXB25x/clustalw_2.1+lgpl-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QCIXB25x/clustalw_2.1+lgpl-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QCIXB25x/clustalw_2.1+lgpl-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QCIXB25x/b1/clustalw_2.1+lgpl-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QCIXB25x/b2/clustalw_2.1+lgpl-7_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 215ms CPU time consumed: 169ms Memory peak: 18.2M (swap: 0B) Thu Sep 4 11:48:50 UTC 2025 I: diffoscope 305 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 4 11:48:50 UTC 2025 I: clustalw from forky built successfully and reproducibly on arm64. Thu Sep 4 11:48:51 UTC 2025 I: Removing signed clustalw_2.1+lgpl-7_arm64.buildinfo.asc files: removed './b1/clustalw_2.1+lgpl-7_arm64.buildinfo.asc' removed './b2/clustalw_2.1+lgpl-7_arm64.buildinfo.asc'