Sun May 5 14:51:59 UTC 2024 I: starting to build rate4site/trixie/arm64 on jenkins on '2024-05-05 14:51' Sun May 5 14:51:59 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/15275/console.log Sun May 5 14:51:59 UTC 2024 I: Downloading source for trixie/rate4site=3.0.0-8 --2024-05-05 14:51:59-- http://deb.debian.org/debian/pool/main/r/rate4site/rate4site_3.0.0-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2054 (2.0K) [text/prs.lines.tag] Saving to: ‘rate4site_3.0.0-8.dsc’ 0K .. 100% 211M=0s 2024-05-05 14:51:59 (211 MB/s) - ‘rate4site_3.0.0-8.dsc’ saved [2054/2054] Sun May 5 14:51:59 UTC 2024 I: rate4site_3.0.0-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rate4site Binary: rate4site Architecture: any Version: 3.0.0-8 Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan , Andreas Tille Homepage: https://www.tau.ac.il/~itaymay/cp/rate4site.html Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/rate4site Vcs-Git: https://salsa.debian.org/med-team/rate4site.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: rate4site deb science optional arch=any Checksums-Sha1: 837fb82c4ac368ebc64a5d8697706be3b0679829 303488 rate4site_3.0.0.orig.tar.gz bb0429162f4a7752031730289dfa5cd8fe7901d0 4684 rate4site_3.0.0-8.debian.tar.xz Checksums-Sha256: 5f748131bc2d10383c35c3141a835efa4ec1e7088cd9d8970e8024021aa509ac 303488 rate4site_3.0.0.orig.tar.gz 66fe3297b77dabf92715dd161c1267cfaa141027385c491279a12532cd3a4165 4684 rate4site_3.0.0-8.debian.tar.xz Files: c06ec2429d1535bf91e8dbcaed537d30 303488 rate4site_3.0.0.orig.tar.gz c1c1e4f19082338f936827542fbfb816 4684 rate4site_3.0.0-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHpQBwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF7Bg/+LWVA7p8SIXXvBqeshe9KiQQtMYG5TDN7 gGjs/gp8cIMu/slAUdfdKE8vMMvnsCoLqDCsmR29I+f8BA+ulJLfd24uyS3lXpYb qYYQrKFG5iyfd823hlfeKFrMOjYBakL0TZIEL/uk4jBW4F0duAT1Spdb2AvkNbnN MjhFQiPRug2WW0+Uf8HJnON1rOOTEWMDyfG9Lk15B6tjMbLIc/fVOZkLFco5Wt0Q 7ctsMGwGL1KxRyH7QGINyiljOV0Kog8GpgEs+Q0QfwW4OksfMoiZQs60WK/yHqje QDHAHeo4xICjn5mhpvqHkkPLWdS60W/bb6hFdbYf/sTC9GtdT2mQfANVKzaUpSVj ABdY/hicvJ4CDLi/lEvivpchscq6lCRm20Cw3DEo5jFu4CAkSiyl6jMzMwlpkSG7 zjkCIvzF6TKJ3JU5Lfueh07r//eDa0TDkjKBnMIoAorfghy2PUll08LG5NNBriP1 nWtGcuIZ1b2K+0b0Imt8QuiPjBW+aLpf28fFrpUAG9YkVOjnEtRrN7rwlW39sP35 fbNvAoSovG1HC4wRHpAv+bZSWHh3p/oyjeTR+ztSYGC3GgpoAQbeqiKJD2XIxBVb 3F3qtAcF5GX2YA7d9Zq2A1KzjSWlIU04AtEn+esjx8PMeH1WmoKyrG+RVfGg27te CR7OKb1zcNc= =ZYMf -----END PGP SIGNATURE----- Sun May 5 14:51:59 UTC 2024 I: Checking whether the package is not for us Sun May 5 14:51:59 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Sun May 5 14:51:59 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Sun May 5 14:52:57 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 5 02:52:01 -12 2024 I: pbuilder-time-stamp: 1714920721 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [rate4site_3.0.0-8.dsc] I: copying [./rate4site_3.0.0.orig.tar.gz] I: copying [./rate4site_3.0.0-8.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 20 10:57:32 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rate4site_3.0.0-8.dsc: no acceptable signature found dpkg-source: info: extracting rate4site in rate4site-3.0.0 dpkg-source: info: unpacking rate4site_3.0.0.orig.tar.gz dpkg-source: info: unpacking rate4site_3.0.0-8.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/535080/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7ae673daeea94778af116466f9995bee' 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='535080' 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.v21MiQpK/pbuilderrc_7qoB --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.v21MiQpK/b1 --logfile b1/build.log rate4site_3.0.0-8.dsc' SUDO_GID='109' 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 codethink02-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 3 08:22 /bin -> usr/bin I: user script /srv/workspace/pbuilder/535080/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 ... 19736 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} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{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, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After unpacking 75.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Fetched 18.7 MB in 0s (130 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19736 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-19) ... 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/rate4site-3.0.0/ && 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 > ../rate4site_3.0.0-8_source.changes dpkg-buildpackage: info: source package rate4site dpkg-buildpackage: info: source version 3.0.0-8 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:5: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:5: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:745: AM_CONFIG_HEADER is expanded from... configure.ac:5: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:8: installing './compile' 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 for a BSD-compatible install... /usr/bin/install -c 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 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 ./configure: line 4526: test: syntax error: `-O2' unexpected 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... unsupported checking for g++ option to enable C++98 features... none needed checking dependency style of g++... none 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 string... yes checking for iostream... yes checking for size_t... yes checking whether the compiler supports GNU C++... (cached) yes checking whether g++ accepts -g... (cached) yes checking for g++ option to enable C++11 features... (cached) unsupported checking for g++ option to enable C++98 features... (cached) none needed checking dependency style of g++... (cached) none checking whether the compiler supports GNU C++... (cached) yes checking whether g++ accepts -g... (cached) yes checking for g++ option to enable C++11 features... (cached) unsupported checking for g++ option to enable C++98 features... (cached) none needed checking dependency style of g++... (cached) none checking for ranlib... ranlib checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/phylogeny/Makefile config.status: creating src/rate4site/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0' make all-recursive make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0' Making all in src/phylogeny make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o alphabet.o alphabet.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o sequenceContainer.o sequenceContainer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o sequence.o sequence.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o mulAlphabet.o mulAlphabet.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o someUtil.o someUtil.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o logFile.o logFile.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o gainLossAlphabet.o gainLossAlphabet.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o pijAccelerator.o pijAccelerator.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o replacementModel.o replacementModel.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o distribution.o distribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o readTree.o readTree.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o errorMsg.o errorMsg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o nucleotide.o nucleotide.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o amino.o amino.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o codon.o codon.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o doubleRep.o doubleRep.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o uniDistribution.o uniDistribution.cpp someUtil.cpp: In function 'void createDir(const std::string&, const std::string&)': someUtil.cpp:507:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 507 | system(sysCall.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o readDatMatrix.o readDatMatrix.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o datMatrixHolder.o datMatrixHolder.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o nucJC.o nucJC.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o aaJC.o aaJC.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o gtrModel.o gtrModel.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o fromQtoPt.o fromQtoPt.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o distanceTable.o distanceTable.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o nj.o nj.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o njConstrain.o njConstrain.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o numRec.o numRec.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o uniformDistribution.o uniformDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o computePijComponent.o computePijComponent.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o stochasticProcess.o stochasticProcess.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o suffStatComponent.o suffStatComponent.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o unObservableData.o unObservableData.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o likeDist.o likeDist.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o countTableComponent.o countTableComponent.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o fastStartTree.o fastStartTree.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o bestAlpha.o bestAlpha.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o gammaDistribution.o gammaDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o siteSpecificRate.o siteSpecificRate.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o recognizeFormat.o recognizeFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o bblEM.o bblEM.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o hky.o hky.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o bestGtrModelParams.o bestGtrModelParams.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o tamura92.o tamura92.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o bestHKYparam.o bestHKYparam.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o bestTamura92param.o bestTamura92param.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o talRandom.o talRandom.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o computeCounts.o computeCounts.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o computeDownAlg.o computeDownAlg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o computeUpAlg.o computeUpAlg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o gammaUtilities.o gammaUtilities.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o treeUtil.o treeUtil.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o matrixUtils.o matrixUtils.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o simulateJumps.o simulateJumps.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o treeIt.o treeIt.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o tree.o tree.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o phylipFormat.o phylipFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o maseFormat.o maseFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o clustalFormat.o clustalFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o fastaFormat.o fastaFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o molphyFormat.o molphyFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o getRandomWeights.o getRandomWeights.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o nexusFormat.o nexusFormat.cpp rm -f libphylo.a ar cru libphylo.a alphabet.o sequenceContainer.o sequence.o mulAlphabet.o someUtil.o logFile.o gainLossAlphabet.o pijAccelerator.o replacementModel.o distribution.o readTree.o errorMsg.o nucleotide.o amino.o geneticCodeHolder.o codon.o doubleRep.o evaluateCharacterFreq.o uniDistribution.o generalGammaDistribution.o readDatMatrix.o datMatrixHolder.o chebyshevAccelerator.o nucJC.o aaJC.o gtrModel.o fromQtoPt.o distanceTable.o nj.o njConstrain.o numRec.o uniformDistribution.o computePijComponent.o stochasticProcess.o suffStatComponent.o unObservableData.o likeDist.o countTableComponent.o fastStartTree.o likelihoodComputationFactors.o bestAlpha.o gammaDistribution.o siteSpecificRate.o likelihoodComputation.o recognizeFormat.o bblEM.o hky.o bestGtrModelParams.o tamura92.o bestHKYparam.o bestTamura92param.o talRandom.o computeSubstitutionCounts.o fromCountTableComponentToDistance.o computeCounts.o computeDownAlg.o computeUpAlg.o computeUpAlgFactors.o gammaUtilities.o seqContainerTreeMap.o treeUtil.o matrixUtils.o simulateCodonsJumps.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o multipleStochasticProcess.o simulateJumps.o simulateJumpsAbstract.o treeIt.o likelihoodComputationGL.o tree.o bblEMProportionalEB.o fromCountTableComponentToDistancePropEB.o likeDistPropEB.o bblLSProportionalEB.o phylipFormat.o maseFormat.o clustalFormat.o fastaFormat.o phylipSequentialFormat.o molphyFormat.o getRandomWeights.o nexusFormat.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libphylo.a make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' Making all in src/rate4site make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' g++ -DHAVE_CONFIG_H -I. -I../.. -DDOUBLEREP -Wdate-time -D_FORTIFY_SOURCE=2 -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o rate4site-rate4siteOptions.o `test -f 'rate4siteOptions.cpp' || echo './'`rate4siteOptions.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -DDOUBLEREP -Wdate-time -D_FORTIFY_SOURCE=2 -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o rate4site-rate4site.o `test -f 'rate4site.cpp' || echo './'`rate4site.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o rate4siteOptions.o rate4siteOptions.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -c -o rate4site.o rate4site.cpp sed -e 's|__pkgdatadir__|/usr/share/rate4site|g;s|__examplesdir__||g;s|__sysconfdir__|/etc|g;s|__bindir__|/usr/bin|g;s|__PACKAGE_VERSION__|3.0.0|g' "rate4site.cpp" | \ pod2man --utf8 -c 'User Commands' -r "3.0.0" -name RATE4SITE > "rate4site.1" g++ -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -Wl,-z,relro -Wl,-z,now -o rate4site_doublerep rate4siteOptions.o rate4site.o ../../src/phylogeny/libphylo.a g++ -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++98 -g -Wl,-z,relro -Wl,-z,now -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0' make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' make[1]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0' Making check in src/phylogeny make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' Making check in src/rate4site make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0' make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' make[1]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rate4site/ make -j12 install DESTDIR=/build/reproducible-path/rate4site-3.0.0/debian/rate4site AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0' Making install in src/phylogeny make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' /usr/bin/mkdir -p '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/lib/aarch64-linux-gnu' /usr/bin/install -c -m 644 libphylo.a '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 replacementMatrixSource/mitochondriaAscidian.code replacementMatrixSource/mitochondriaProtozoan.code replacementMatrixSource/nuclearCiliate.code replacementMatrixSource/mitochondriaEchinoderm.code replacementMatrixSource/mitochondriaVertebrate.code replacementMatrixSource/nuclearEuplotid.code replacementMatrixSource/mitochondriaFlatworm.code replacementMatrixSource/mitochondriaYeast.code replacementMatrixSource/nuclearStandard.code replacementMatrixSource/mitochondriaInvertebrate.code replacementMatrixSource/nuclearBlepharisma.code cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q adrianCodon.dat.q LG.dat.q replacementMatrixSource/cpREV45.dat replacementMatrixSource/dayhoff.dat replacementMatrixSource/jones.dat replacementMatrixSource/mtREV24.dat replacementMatrixSource/wag.dat getopt.h errorMsg.h definitions.h doubleRep.h ConversionUtils.h sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h pijAccelerator.h replacementModel.h distribution.h '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 readTree.h nucleotide.h amino.h geneticCodeHolder.h codon.h evaluateCharacterFreq.h uniDistribution.h generalGammaDistribution.h readDatMatrix.h datMatrixHolder.h chebyshevAccelerator.h nucJC.h aaJC.h gtrModel.h fromQtoPt.h trivialAccelerator.h distanceMethod.h distanceTable.h nj.h njConstrain.h distances2Tree.h numRec.h uniformDistribution.h checkcovFanctors.h likelihoodComputation.h computePijComponent.h stochasticProcess.h suffStatComponent.h unObservableData.h likeDist.h countTableComponent.h jcDistance.h fastStartTree.h checkcovFanctorsWithFactors.h likelihoodComputationFactors.h bestAlpha.h gammaDistribution.h siteSpecificRate.h recognizeFormat.h bblEM.h '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 bestGtrModelParams.h tamura92.h bestHKYparam.h hky.h bestTamura92param.h talRandom.h computeSubstitutionCounts.h fromCountTableComponentToDistance.h computeCounts.h computeDownAlg.h computeUpAlg.h gammaUtilities.h seqContainerTreeMap.h treeUtil.h matrixUtils.h computePosteriorExpectationOfSubstitutions.h computePosteriorExpectationOfSubstitutions_nonReversibleSp.h multipleStochasticProcess.h simulateJumps.h simulateJumpsAbstract.h simulateCodonsJumps.h treeIt.h likelihoodComputationGL.h tree.h bblEMProportionalEB.h fromCountTableComponentToDistancePropEB.h likeDistPropEB.h bblLSProportionalEB.h phylipFormat.h maseFormat.h clustalFormat.h fastaFormat.h phylipSequentialFormat.h molphyFormat.h getRandomWeights.h nexusFormat.h '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' ( cd '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/lib/aarch64-linux-gnu' && ranlib libphylo.a ) make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' Making install in src/rate4site make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' /usr/bin/mkdir -p '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/share/man/man1' /usr/bin/install -c rate4site rate4site_doublerep '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/bin' /usr/bin/install -c -m 644 rate4site.1 '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0' make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0' 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/rate4site-3.0.0' make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' make[1]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rate4site' in '../rate4site_3.0.0-8_arm64.deb'. dpkg-deb: building package 'rate4site-dbgsym' in '../rate4site-dbgsym_3.0.0-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rate4site_3.0.0-8_arm64.buildinfo dpkg-genchanges --build=binary -O../rate4site_3.0.0-8_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/535080 and its subdirectories I: Current time: Sun May 5 02:52:56 -12 2024 I: pbuilder-time-stamp: 1714920776 Sun May 5 14:52:58 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sun May 5 14:52:58 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sun May 5 14:54:01 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sun May 5 14:54:02 UTC 2024 I: rate4site_3.0.0-8_arm64.changes: Format: 1.8 Date: Thu, 20 Jan 2022 11:42:04 +0100 Source: rate4site Binary: rate4site rate4site-dbgsym Architecture: arm64 Version: 3.0.0-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: rate4site - detector of conserved amino-acid sites Changes: rate4site (3.0.0-8) unstable; urgency=medium . * Upstream download vanished * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: 1515180d641bbf6a33734fd1d4a777653c50023e 9468216 rate4site-dbgsym_3.0.0-8_arm64.deb b06f8b72162580ffb0027315c7531540dac3ea13 5106 rate4site_3.0.0-8_arm64.buildinfo 93dee5295914fd8fdf71907268f9720620f1b0de 583068 rate4site_3.0.0-8_arm64.deb Checksums-Sha256: c26a3d3be6dc9966e63fdc236153d919de4393922aa63a8aaf7fde75d8f1a186 9468216 rate4site-dbgsym_3.0.0-8_arm64.deb 09b802eedb146a5217addaa8023d540ccee25086bba495b0ff79fa66875fd7c5 5106 rate4site_3.0.0-8_arm64.buildinfo 0ad94edc19d03c3986e971e0e8ee05e7afb28b25a4b1ce3addedece5d85891c4 583068 rate4site_3.0.0-8_arm64.deb Files: 5709d8a3be8430ca896edce25d9bb204 9468216 debug optional rate4site-dbgsym_3.0.0-8_arm64.deb bbd5c5731b0b49f8afd598efda0a2639 5106 science optional rate4site_3.0.0-8_arm64.buildinfo d885a705afda87b908aaa49d7d7cc883 583068 science optional rate4site_3.0.0-8_arm64.deb Sun May 5 14:54:03 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_7-15275.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.v21MiQpK/rate4site_3.0.0-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.v21MiQpK/rate4site_3.0.0-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.v21MiQpK/rate4site_3.0.0-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.v21MiQpK/b1/rate4site_3.0.0-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.v21MiQpK/b2/rate4site_3.0.0-8_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 abc.DotChangesFile ## main (total time: 0.479s) 0.479s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.118s) 0.118s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 814ms CPU time consumed: 809ms Sun May 5 14:54:04 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sun May 5 14:54:04 UTC 2024 I: rate4site from trixie built successfully and reproducibly on arm64. Sun May 5 14:54:06 UTC 2024 I: Submitting .buildinfo files to external archives: Sun May 5 14:54:06 UTC 2024 I: Submitting 8.0K b1/rate4site_3.0.0-8_arm64.buildinfo.asc Sun May 5 14:54:07 UTC 2024 I: Submitting 8.0K b2/rate4site_3.0.0-8_arm64.buildinfo.asc Sun May 5 14:54:07 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 5 14:54:07 UTC 2024 I: Done submitting .buildinfo files. Sun May 5 14:54:07 UTC 2024 I: Removing signed rate4site_3.0.0-8_arm64.buildinfo.asc files: removed './b1/rate4site_3.0.0-8_arm64.buildinfo.asc' removed './b2/rate4site_3.0.0-8_arm64.buildinfo.asc'