I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 6 19:40:34 -12 2023 I: pbuilder-time-stamp: 1686123634 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [phylonium_1.6-1.dsc] I: copying [./phylonium_1.6.orig-debian-tests-data.tar.gz] I: copying [./phylonium_1.6.orig.tar.gz] I: copying [./phylonium_1.6-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 30 01:41:09 2021 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phylonium_1.6-1.dsc: no acceptable signature found dpkg-source: info: extracting phylonium in phylonium-1.6 dpkg-source: info: unpacking phylonium_1.6.orig.tar.gz dpkg-source: info: unpacking phylonium_1.6.orig-debian-tests-data.tar.gz dpkg-source: info: unpacking phylonium_1.6-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1527/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=8 ' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='1527' 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.JICTG5Kn/pbuilderrc_mIdW --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JICTG5Kn/b1 --logfile b1/build.log phylonium_1.6-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink10-arm64 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 4 22:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1527/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), libdivsufsort-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19611 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev 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} libdivsufsort-dev{a} libdivsufsort3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{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, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 18.4 MB of archives. After unpacking 74.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libdivsufsort3 arm64 2.0.1-5 [38.9 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libdivsufsort-dev arm64 2.0.1-5 [19.1 kB] Fetched 18.4 MB in 1s (36.6 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 ... 19611 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... 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_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... 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 libelf1:arm64. Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... 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_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libdivsufsort3:arm64. Preparing to unpack .../30-libdivsufsort3_2.0.1-5_arm64.deb ... Unpacking libdivsufsort3:arm64 (2.0.1-5) ... Selecting previously unselected package libdivsufsort-dev:arm64. Preparing to unpack .../31-libdivsufsort-dev_2.0.1-5_arm64.deb ... Unpacking libdivsufsort-dev:arm64 (2.0.1-5) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libdivsufsort3:arm64 (2.0.1-5) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up libdivsufsort-dev:arm64 (2.0.1-5) ... 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 (0.21-12) ... Setting up libtool (2.4.7-5) ... 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 dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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/phylonium-1.6/ && 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 > ../phylonium_1.6-1_source.changes dpkg-buildpackage: info: source package phylonium dpkg-buildpackage: info: source version 1.6-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Fabian Klötzl 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:11: installing './ar-lib' configure.ac:6: installing './compile' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' parallel-tests: installing './test-driver' libs/Makefile.am: installing './depcomp' test/Makefile.am:7: warning: source file '$(top_srcdir)/src/esa.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. test/Makefile.am:7: warning: source file '$(top_srcdir)/src/evo_model.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/process.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/sequence.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled debian/rules override_dh_auto_configure make[1]: Entering directory '/build/phylonium-1.6' dh_auto_configure -- --disable-x86simd ./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 --disable-x86simd 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 checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking whether make sets $(MAKE)... (cached) yes checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for g++ option to support OpenMP... -fopenmp checking whether g++ supports C++14 features with -std=gnu++14... yes checking for gcc option to support OpenMP... -fopenmp checking for __attribute__((ifunc))... yes checking for cos in -lm... yes 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 divsufsort.h... yes checking for divsufsort in -ldivsufsort... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking for err.h... yes checking for errno.h... yes checking for fcntl.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int32_t... yes checking for uint8_t... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking for strtod... yes checking for reallocarray... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating libs/Makefile config.status: creating Makefile config.status: creating man/phylonium.1 config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/phylonium-1.6' dh_auto_build make -j8 make[1]: Entering directory '/build/phylonium-1.6' make all-recursive make[2]: Entering directory '/build/phylonium-1.6' Making all in libs make[3]: Entering directory '/build/phylonium-1.6/libs' rm -f libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -I../opt -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c ar cru libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o revseqcmp.o revseqcmp.c ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqcmp.o seqcmp.c rm -f librevseqcmp.a ar cru librevseqcmp.a revseqcmp.o rm -f libseqcmp.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib librevseqcmp.a ar cru libseqcmp.a seqcmp.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp.a rm -f libpfasta.a ar cru libpfasta.a libpfasta_a-pfasta.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpfasta.a make[3]: Leaving directory '/build/phylonium-1.6/libs' Making all in src make[3]: Entering directory '/build/phylonium-1.6/src' g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-phylonium.o `test -f 'phylonium.cxx' || echo './'`phylonium.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-io.o `test -f 'io.cxx' || echo './'`io.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-sequence.o `test -f 'sequence.cxx' || echo './'`sequence.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-esa.o `test -f 'esa.cxx' || echo './'`esa.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-process.o `test -f 'process.cxx' || echo './'`process.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-evo_model.o `test -f 'evo_model.cxx' || echo './'`evo_model.cxx esa.cxx: In constructor 'esa::esa(const sequence&)': esa.cxx:63:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'int' [-Wnarrowing] 63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ g++ -std=gnu++14 -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phylonium phylonium-phylonium.o phylonium-io.o phylonium-sequence.o phylonium-esa.o phylonium-process.o phylonium-evo_model.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a -ldivsufsort -lm make[3]: Leaving directory '/build/phylonium-1.6/src' Making all in test make[3]: Entering directory '/build/phylonium-1.6/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/phylonium-1.6/test' Making all in . make[3]: Entering directory '/build/phylonium-1.6' make[3]: Leaving directory '/build/phylonium-1.6' make[2]: Leaving directory '/build/phylonium-1.6' make[1]: Leaving directory '/build/phylonium-1.6' dh_auto_test make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 make[1]: Entering directory '/build/phylonium-1.6' Making check in libs make[2]: Entering directory '/build/phylonium-1.6/libs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/phylonium-1.6/libs' Making check in src make[2]: Entering directory '/build/phylonium-1.6/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/phylonium-1.6/src' Making check in test make[2]: Entering directory '/build/phylonium-1.6/test' make simf unittests make[3]: Entering directory '/build/phylonium-1.6/test' g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simf-simf.o `test -f 'simf.cxx' || echo './'`simf.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-esa.o `test -f '../src/esa.cxx' || echo './'`../src/esa.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-evo_model.o `test -f '../src/evo_model.cxx' || echo './'`../src/evo_model.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-process.o `test -f '../src/process.cxx' || echo './'`../src/process.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tmain.o `test -f 'Tmain.cxx' || echo './'`Tmain.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tprocess.o `test -f 'Tprocess.cxx' || echo './'`Tprocess.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.cxx ../src/process.cxx:420: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 420 | #pragma omp parallel for num_threads(THREADS) | ../src/process.cxx:432: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 432 | #pragma omp critical | ../src/process.cxx:435: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 435 | #pragma omp atomic | ../src/process.cxx:441: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 441 | #pragma omp critical | ../src/process.cxx:511: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 511 | #pragma omp parallel for num_threads(THREADS) | ../src/process.cxx:518: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 518 | #pragma omp atomic | ../src/process.cxx:526: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 526 | #pragma omp atomic read | ../src/process.cxx:532: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 532 | #pragma omp critical | ../src/esa.cxx: In constructor 'esa::esa(const sequence&)': ../src/esa.cxx:63:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'int' [-Wnarrowing] 63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ g++ -std=gnu++14 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort -lm g++ -std=gnu++14 -ggdb -g -O2 -ffile-prefix-map=/build/phylonium-1.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o unittests unittests-esa.o unittests-evo_model.o unittests-process.o unittests-sequence.o unittests-Tmain.o unittests-Tprocess.o unittests-Tsequence.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a -ldivsufsort -lm make[3]: Leaving directory '/build/phylonium-1.6/test' make[2]: Leaving directory '/build/phylonium-1.6/test' Making check in . make[2]: Entering directory '/build/phylonium-1.6' make check-TESTS make[3]: Entering directory '/build/phylonium-1.6' make[4]: Entering directory '/build/phylonium-1.6' PASS: test/unittests PASS: test/simple.sh ============================================================================ Testsuite summary for phylonium 1.6 ============================================================================ # TOTAL: 2 # PASS: 2 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/phylonium-1.6' make[3]: Leaving directory '/build/phylonium-1.6' make[2]: Leaving directory '/build/phylonium-1.6' make[1]: Leaving directory '/build/phylonium-1.6' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phylonium/ make -j8 install DESTDIR=/build/phylonium-1.6/debian/phylonium AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/phylonium-1.6' Making install in libs make[2]: Entering directory '/build/phylonium-1.6/libs' make[3]: Entering directory '/build/phylonium-1.6/libs' 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/phylonium-1.6/libs' make[2]: Leaving directory '/build/phylonium-1.6/libs' Making install in src make[2]: Entering directory '/build/phylonium-1.6/src' make[3]: Entering directory '/build/phylonium-1.6/src' /usr/bin/mkdir -p '/build/phylonium-1.6/debian/phylonium/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c phylonium '/build/phylonium-1.6/debian/phylonium/usr/bin' make[3]: Leaving directory '/build/phylonium-1.6/src' make[2]: Leaving directory '/build/phylonium-1.6/src' Making install in test make[2]: Entering directory '/build/phylonium-1.6/test' make[3]: Entering directory '/build/phylonium-1.6/test' 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/phylonium-1.6/test' make[2]: Leaving directory '/build/phylonium-1.6/test' Making install in . make[2]: Entering directory '/build/phylonium-1.6' make[3]: Entering directory '/build/phylonium-1.6' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/phylonium-1.6/debian/phylonium/usr/share/doc/phylonium' /usr/bin/mkdir -p '/build/phylonium-1.6/debian/phylonium/usr/share/man/man1' /usr/bin/install -c -m 644 documentation/manual.pdf '/build/phylonium-1.6/debian/phylonium/usr/share/doc/phylonium' /usr/bin/install -c -m 644 man/phylonium.1 '/build/phylonium-1.6/debian/phylonium/usr/share/man/man1' make[3]: Leaving directory '/build/phylonium-1.6' make[2]: Leaving directory '/build/phylonium-1.6' make[1]: Leaving directory '/build/phylonium-1.6' dh_installdocs dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping 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 'phylonium' in '../phylonium_1.6-1_arm64.deb'. dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.6-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../phylonium_1.6-1_arm64.buildinfo dpkg-genchanges --build=binary -O../phylonium_1.6-1_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: 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/1527 and its subdirectories I: Current time: Tue Jun 6 19:44:12 -12 2023 I: pbuilder-time-stamp: 1686123852