Wed Sep 10 12:03:02 UTC 2025 I: starting to build prank/forky/amd64 on jenkins on '2025-09-10 12:02' Wed Sep 10 12:03:02 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/71651/console.log Wed Sep 10 12:03:02 UTC 2025 I: Downloading source for forky/prank=250331-1 --2025-09-10 12:03:02-- http://deb.debian.org/debian/pool/main/p/prank/prank_250331-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1977 (1.9K) [text/prs.lines.tag] Saving to: ‘prank_250331-1.dsc’ 0K . 100% 219M=0s 2025-09-10 12:03:02 (219 MB/s) - ‘prank_250331-1.dsc’ saved [1977/1977] Wed Sep 10 12:03:02 UTC 2025 I: prank_250331-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prank Binary: prank Architecture: any Version: 250331-1 Maintainer: Debian Med Packaging Team Uploaders: Manuel Prinz , Andreas Tille Homepage: https://ariloytynoja.github.io/prank-msa/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/prank Vcs-Git: https://salsa.debian.org/med-team/prank.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: prank deb science optional arch=any Checksums-Sha1: 47df16d7f031b28597ea05fb29c1c489b75abc13 158741 prank_250331.orig.tar.gz 482cfc957c418498b3a70235245bc0d9771d4690 19484 prank_250331-1.debian.tar.xz Checksums-Sha256: 4847b565eae3b99feaee2f53c0583a384c8fe3552b00cd019fca9ce4bff113b9 158741 prank_250331.orig.tar.gz 656ab0531952dbd7511f7f3ccff1fbfdf59ede5aac3a1038dce0f58ef1243ff3 19484 prank_250331-1.debian.tar.xz Files: 342a0711afcad2977b958643942042a2 158741 prank_250331.orig.tar.gz d3bf5c851ca1a6d1c8841aea1e492624 19484 prank_250331-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEc0cUmcxg7Z7ugFlGxb1sjyKV1QIFAmi+H+0SHHBsZXNzeUBk ZWJpYW4ub3JnAAoJEMW9bI8ildUCM/gP/RrDzMlgBj4vdexM9/5QHugyBokhDg+N s2rre8dqoVxzXUAOO7VfTdp4mGMnO6Y/OTWPR235owFisdwqgfJYPx7tE8jQ+pEg wgLwv2Q1MACh43BS82P6jc/Zo/cQrGZLTj0T8I/5UTzcg4OonKplbcbxNGYYtqqr 7sPpeyeVNhFDfhGBg0LJLY6U9hg2yAAzEF6MF7yLr5Zwahl+BytoGp6Y/RG1L+pq 3hOOfC4+u1iAkqq98WZuQn0lUX+TDgNZTiHFX9kFdnqMXPkW2IVWvrGFIJljgnAe X9N6A9R9rFDJ8UCBw5CQIe0385fu3NdrkBC4ZQdvtMnkRo9ZWD+60bcN26mnO9Xa ZHiye888Dz6+U1e0Yixiw3zjAy8q21wDkZinojVej6jbuiwyNcttzUWNufWltG7e xVcDVBBAhHb6GsnFqk/pD4MzGdhV0fFwcI2zufyvZnyySFw9XQGJ6kEyc8lUOyXA A972lLtHHlUmi4BB7aNRbw4eyXAd08HEBldDCcOYE/jr2hisNn2HQ9eLsztVX35x A/+pNz6rKDNjj3dMBu0tbFZI5O1qbgNM1+dWTUhj0ocYJ6277y/R7FajLcVBpkTw SXZKeWkfBDmcqkctbr7pobgOaMMUrfofSxeYwpesmMUXAZQxLjbWFayCkHxdiA/o OV6asQwu/Yjg =Id7B -----END PGP SIGNATURE----- Wed Sep 10 12:03:02 UTC 2025 I: Checking whether the package is not for us Wed Sep 10 12:03:02 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed Sep 10 12:03:02 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed Sep 10 12:04:32 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 10 00:03:03 -12 2025 I: pbuilder-time-stamp: 1757505783 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 [prank_250331-1.dsc] I: copying [./prank_250331.orig.tar.gz] I: copying [./prank_250331-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./prank_250331-1.dsc: no acceptable signature found dpkg-source: info: extracting prank in prank-250331 dpkg-source: info: unpacking prank_250331.orig.tar.gz dpkg-source: info: unpacking prank_250331-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3742893/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e924aab10b43498382b1691a20dfc76d' 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='3742893' 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.oLFH0qYv/pbuilderrc_SOEP --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.oLFH0qYv/b1 --logfile b1/build.log prank_250331-1.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3742893/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 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 11.2 MB of archives. After unpacking 42.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-2 [95.0 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.14.2-1 [19.8 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.14.2-1 [8768 B] Get: 22 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Fetched 11.2 MB in 1s (20.4 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 ... 19897 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_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-2_amd64.deb ... Unpacking bsdextrautils (2.41.1-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.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:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.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:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-2) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (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:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... 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/prank-250331/ && 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 > ../prank_250331-1_source.changes dpkg-buildpackage: info: source package prank dpkg-buildpackage: info: source version 250331-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Charles Plessy dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/prank-250331' # No distclean! See README.source ( cd src ; make clean ) make[2]: Entering directory '/build/reproducible-path/prank-250331/src' rm -f writefile.o treenode.o translatesequences.o terminalsequence.o terminalnode.o site.o sequence.o readnewick.o readfile.o readalignment.o pwsite.o pwhirschberg.o progressivealignment.o prank.o postprobability.o phylomatchscore.o node.o intmatrix.o hmmodel.o hirschberg.o guidetree.o fullprobability.o flmatrix.o eigen.o dbmatrix.o characterprobability.o boolmatrix.o ancestralsequence.o ancestralnode.o check_version.o exonerate_reads.o mafft_alignment.o bppancestors.o raxmlancestors.o fasttree_tree.o raxmlrebl.o rm -f *~ core *.core make[2]: Leaving directory '/build/reproducible-path/prank-250331/src' ( cd src ; rm -f prank prank.1 ) make[1]: Leaving directory '/build/reproducible-path/prank-250331' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/prank-250331' dh_auto_build --verbose cd src && make -j40 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/prank-250331/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o writefile.o writefile.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o treenode.o treenode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o translatesequences.o translatesequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o terminalsequence.o terminalsequence.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o terminalnode.o terminalnode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o site.o site.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o sequence.o sequence.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o readnewick.o readnewick.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o readfile.o readfile.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o readalignment.o readalignment.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o pwsite.o pwsite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o pwhirschberg.o pwhirschberg.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o progressivealignment.o progressivealignment.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o prank.o prank.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o postprobability.o postprobability.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o phylomatchscore.o phylomatchscore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o node.o node.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o intmatrix.o intmatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o hmmodel.o hmmodel.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o hirschberg.o hirschberg.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o guidetree.o guidetree.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o fullprobability.o fullprobability.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o flmatrix.o flmatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o eigen.o eigen.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o dbmatrix.o dbmatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o characterprobability.o characterprobability.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o boolmatrix.o boolmatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o ancestralsequence.o ancestralsequence.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o ancestralnode.o ancestralnode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o check_version.o check_version.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o exonerate_reads.o exonerate_reads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o mafft_alignment.o mafft_alignment.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o bppancestors.o bppancestors.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o raxmlancestors.o raxmlancestors.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o fasttree_tree.o fasttree_tree.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-250331=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I/usr/include -o raxmlrebl.o raxmlrebl.cpp pod2man --utf8 --center "The Probabilistic Alignment Kit" -release="v.121211" --section=1 --name="PRANK" prank.1.pod >prank.1 In file included from ancestralnode.h:24, from hmmodel.h:36, from site.cpp:22: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from ancestralsequence.cpp:24: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from translatesequences.cpp:22: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from ancestralnode.cpp:27: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from fasttree_tree.h:8, from guidetree.cpp:23: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from hmmodel.cpp:26: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from terminalsequence.cpp:24: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from terminalnode.h:23, from terminalnode.cpp:22: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from readalignment.h:28, from readalignment.cpp:23: treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from hirschberg.cpp:25: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from characterprobability.cpp:24: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from phylomatchscore.cpp:23: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from postprobability.cpp:23: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from mafft_alignment.cpp:6: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from treenode.cpp:25: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from fullprobability.cpp:25: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from pwhirschberg.cpp:25: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from fasttree_tree.h:8, from fasttree_tree.cpp:21: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from exonerate_reads.cpp:10: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from bppancestors.h:24, from bppancestors.cpp:29: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from readnewick.h:29, from progressivealignment.cpp:28: treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, from progressivealignment.h:30, from prank.cpp:29: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from readnewick.h:29, from readnewick.cpp:27: treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from writefile.h:25, from writefile.cpp:27: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from raxmlrebl.h:24, from raxmlrebl.cpp:30: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, from raxmlancestors.h:24, from raxmlancestors.cpp:30: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:365:63: warning: no return statement in function returning non-void [-Wreturn-type] 365 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ ancestralnode.cpp: In member function 'std::string AncestralNode::getThisAncCharactersAt(int)': ancestralnode.cpp:1546:1: warning: control reaches end of non-void function [-Wreturn-type] 1546 | } | ^ guidetree.cpp: In member function 'void GuideTree::computeTree(std::vector >*, std::vector >*, IntMatrix*)': guidetree.cpp:164:37: warning: '%i' directive writing between 1 and 10 bytes into a region of size between 6 and 15 [-Wformat-overflow=] 164 | sprintf(prop,"%i to %i",i,j); | ^~ guidetree.cpp:164:30: note: directive argument in the range [1, 2147483647] 164 | sprintf(prop,"%i to %i",i,j); | ^~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from guidetree.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'void GuideTree::computeTree(std::vector >*, std::vector >*, IntMatrix*)' at guidetree.cpp:164:24: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 25 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ hmmodel.cpp: In member function 'void HMModel::readModel(const char*)': hmmodel.cpp:338:31: warning: '%i' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] 338 | sprintf(str,"state%i",l); | ^~ hmmodel.cpp:338:25: note: directive argument in the range [-2147483647, 2147483646] 338 | sprintf(str,"state%i",l); | ^~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from hmmodel.cpp:24: In function 'int sprintf(char*, const char*, ...)', inlined from 'void HMModel::readModel(const char*)' at hmmodel.cpp:338:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o prank writefile.o treenode.o translatesequences.o terminalsequence.o terminalnode.o site.o sequence.o readnewick.o readfile.o readalignment.o pwsite.o pwhirschberg.o progressivealignment.o prank.o postprobability.o phylomatchscore.o node.o intmatrix.o hmmodel.o hirschberg.o guidetree.o fullprobability.o flmatrix.o eigen.o dbmatrix.o characterprobability.o boolmatrix.o ancestralsequence.o ancestralnode.o check_version.o exonerate_reads.o mafft_alignment.o bppancestors.o raxmlancestors.o fasttree_tree.o raxmlrebl.o -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/prank-250331/src' make[1]: Leaving directory '/build/reproducible-path/prank-250331' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install --destdir=debian/prank/ -O--sourcedirectory=src debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/prank-250331' dh_install src/prank /usr/bin dh_installman src/prank.1 make[1]: Leaving directory '/build/reproducible-path/prank-250331' dh_installdocs -O--sourcedirectory=src debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/prank-250331' dh_installchangelogs VERSION_HISTORY make[1]: Leaving directory '/build/reproducible-path/prank-250331' dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'prank' in '../prank_250331-1_amd64.deb'. dpkg-deb: building package 'prank-dbgsym' in '../prank-dbgsym_250331-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../prank_250331-1_amd64.buildinfo dpkg-genchanges --build=binary -O../prank_250331-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full 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/3742893 and its subdirectories I: Current time: Wed Sep 10 00:04:31 -12 2025 I: pbuilder-time-stamp: 1757505871 Wed Sep 10 12:04:32 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed Sep 10 12:04:32 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed Sep 10 12:06:48 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed Sep 10 12:06:48 UTC 2025 I: prank_250331-1_amd64.changes: Format: 1.8 Date: Mon, 08 Sep 2025 09:06:19 +0900 Source: prank Binary: prank prank-dbgsym Architecture: amd64 Version: 250331-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Charles Plessy Description: prank - Probabilistic Alignment Kit for DNA, codon and amino-acid sequenc Changes: prank (250331-1) unstable; urgency=medium . * Team upload. * New upstream release. * Refresh Makefile patch and forward it. * Replace test data file with one from upstream documentation. Checksums-Sha1: 3253e4538f2c46d246426fbbc135f128b359e97e 3847284 prank-dbgsym_250331-1_amd64.deb 91f18b227cf3b20b58adc56c7a35382e14f23a53 4868 prank_250331-1_amd64.buildinfo d213ea6931cb2af6423096e7a72217675c80f197 376124 prank_250331-1_amd64.deb Checksums-Sha256: 9b1b2d44c31f5df94d1f74192e8fbe710adefd6e02d7998200557514812016e6 3847284 prank-dbgsym_250331-1_amd64.deb 7349472eae191df728d78da97ffb4e844defd3b7b3480db1701954b9394d238b 4868 prank_250331-1_amd64.buildinfo 9b6606006eda229ec279ae159c47d616350f7a9f33140e863bc303af13c2fb7f 376124 prank_250331-1_amd64.deb Files: 969c6a0d961569c597ce40905794775e 3847284 debug optional prank-dbgsym_250331-1_amd64.deb 3c8f0b06d3d97e50c91bc43a4c5b81d6 4868 science optional prank_250331-1_amd64.buildinfo 3b68ca221a1d28060acb7592ff7dac31 376124 science optional prank_250331-1_amd64.deb Wed Sep 10 12:06:49 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_23-71651.service; invocation ID: 919ed5ec7e2e4352b661393b3adfdb69 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.oLFH0qYv/prank_250331-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.oLFH0qYv/prank_250331-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.oLFH0qYv/prank_250331-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.oLFH0qYv/b1/prank_250331-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.oLFH0qYv/b2/prank_250331-1_amd64.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: 216ms CPU time consumed: 178ms Memory peak: 17.6M (swap: 0B) Wed Sep 10 12:06:49 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Wed Sep 10 12:06:49 UTC 2025 I: prank from forky built successfully and reproducibly on amd64. Wed Sep 10 12:06:50 UTC 2025 I: Removing signed prank_250331-1_amd64.buildinfo.asc files: removed './b1/prank_250331-1_amd64.buildinfo.asc' removed './b2/prank_250331-1_amd64.buildinfo.asc'