I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 1 10:27:47 +14 2024 I: pbuilder-time-stamp: 1717187267 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [phyx_1.01+ds-2+deb11u1.dsc] I: copying [./phyx_1.01+ds.orig.tar.xz] I: copying [./phyx_1.01+ds-2+deb11u1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.av1AH8su/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 5 11:56:08 2023 +14 gpgv: using RSA key 2DE8E20E24A21FD8ED1B4CA77D83D406A09DC1E4 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phyx_1.01+ds-2+deb11u1.dsc dpkg-source: info: extracting phyx in phyx-1.01+ds dpkg-source: info: unpacking phyx_1.01+ds.orig.tar.xz dpkg-source: info: unpacking phyx_1.01+ds-2+deb11u1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying link_lnlopt.patch dpkg-source: info: applying gcc10.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3403589/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 1 10:27 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3403589/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3403589/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=ab39b103653f48309916b676799e0c60 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3403589 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AiaIY9wx/pbuilderrc_Pq1r --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AiaIY9wx/b2 --logfile b2/build.log phyx_1.01+ds-2+deb11u1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 21 2022 more -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 9 Jun 1 10:27 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 21 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3403589/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libarmadillo-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 ... 19707 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-cxx-dev; however: Package libnlopt-cxx-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-dev; however: Package libnlopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libarmadillo-dev; however: Package libarmadillo-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} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarmadillo-dev{a} libarmadillo10{a} libarpack2{a} libarpack2-dev{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} liblapack-dev{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libsuperlu-dev{a} libsuperlu5{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 37.4 MB of archives. After unpacking 154 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 hdf5-helpers amd64 1.10.6+repack-4+deb11u1 [40.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libaec-dev amd64 1.0.4-1 [18.7 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libarpack2 amd64 3.8.0-1 [103 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libsuperlu5 amd64 5.2.2+dfsg1-2 [163 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libarmadillo10 amd64 1:10.1.2+dfsg-6+b1 [98.8 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libblas-dev amd64 3.9.0-3 [161 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 liblapack-dev amd64 3.9.0-3 [4247 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libarpack2-dev amd64 3.8.0-1 [117 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libhdf5-fortran-102 amd64 1.10.6+repack-4+deb11u1 [105 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-100 amd64 1.10.6+repack-4+deb11u1 [81.8 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-fortran-100 amd64 1.10.6+repack-4+deb11u1 [56.8 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libhdf5-cpp-103-1 amd64 1.10.6+repack-4+deb11u1 [141 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-cpp-100 amd64 1.10.6+repack-4+deb11u1 [37.7 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo-dev amd64 1:2.0.6-4 [278 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libjpeg-dev amd64 1:2.0.6-4 [67.8 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libhdf5-dev amd64 1.10.6+repack-4+deb11u1 [2438 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libsuperlu-dev amd64 5.2.2+dfsg1-2 [21.4 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libarmadillo-dev amd64 1:10.1.2+dfsg-6+b1 [387 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libnlopt0 amd64 2.7.0-4+b2 [172 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libnlopt-dev amd64 2.7.0-4+b2 [29.8 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libnlopt-cxx0 amd64 2.7.0-4+b2 [200 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libnlopt-cxx-dev amd64 2.7.0-4+b2 [14.5 kB] Fetched 37.4 MB in 1s (57.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up libnlopt0:amd64 (2.7.0-4+b2) ... Setting up file (1:5.39-3) ... Setting up libaec0:amd64 (1.0.4-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.0.6-4) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libnlopt-cxx0:amd64 (2.7.0-4+b2) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libnlopt-dev:amd64 (2.7.0-4+b2) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libblas-dev:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.0.4-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up liblapack3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libaec-dev:amd64 (1.0.4-1) ... Setting up libarpack2:amd64 (3.8.0-1) ... Setting up libjpeg-dev:amd64 (1:2.0.6-4) ... Setting up libsuperlu5:amd64 (5.2.2+dfsg1-2) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnlopt-cxx-dev:amd64 (2.7.0-4+b2) ... Setting up liblapack-dev:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libsuperlu-dev:amd64 (5.2.2+dfsg1-2) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libhdf5-hl-100:amd64 (1.10.6+repack-4+deb11u1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libarmadillo10 (1:10.1.2+dfsg-6+b1) ... Setting up libarpack2-dev:amd64 (3.8.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libhdf5-fortran-102:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.6+repack-4+deb11u1) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libhdf5-dev (1.10.6+repack-4+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libarmadillo-dev (1:10.1.2+dfsg-6+b1) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3403589/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/3403589/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/phyx-1.01+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../phyx_1.01+ds-2+deb11u1_source.changes dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 1.01+ds-2+deb11u1 dpkg-buildpackage: info: source distribution bullseye dpkg-buildpackage: info: source changed by Olek Wojnar dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phyx-1.01+ds' rm -rf src/phyx.logfile if [ -r src/Makefile ]; then \ /usr/bin/make -C src distclean; \ fi make[1]: Leaving directory '/build/phyx-1.01+ds' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src cd src && ./configure --build=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for g++... g++ 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for fabs in -lm... yes checking for nlopt_version in -lnlopt... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking nlopt.h usability... yes checking nlopt.h presence... yes checking for nlopt.h... yes checking for library containing wrapper_sgesv_... -larmadillo checking fenv.h usability... yes checking fenv.h presence... yes checking for fenv.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working strtod... yes checking for floor... yes checking for pow... yes checking for sqrt... yes configure: creating ./config.status config.status: creating Makefile config.status: creating config.h dh_auto_build -O--sourcedirectory=src cd src && make -j16 make[1]: Entering directory '/build/phyx-1.01+ds/src' g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "log.d" -o "log.o" "log.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "node.d" -o "node.o" "node.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tree.d" -o "tree.o" "tree.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tree_reader.d" -o "tree_reader.o" "tree_reader.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tree_utils.d" -o "tree_utils.o" "tree_utils.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "sequence.d" -o "sequence.o" "sequence.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_reader.d" -o "seq_reader.o" "seq_reader.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_utils.d" -o "seq_utils.o" "seq_utils.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_models.d" -o "seq_models.o" "seq_models.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "pairwise_alignment.d" -o "pairwise_alignment.o" "pairwise_alignment.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "superdouble.d" -o "superdouble.o" "superdouble.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_mrca.d" -o "main_mrca.o" "main_mrca.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_mrca_cut.d" -o "main_mrca_cut.o" "main_mrca_cut.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_mrca_name.d" -o "main_mrca_name.o" "main_mrca_name.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_consq.d" -o "main_consq.o" "main_consq.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "bd_sim.d" -o "bd_sim.o" "bd_sim.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_bd_sim.d" -o "main_bd_sim.o" "main_bd_sim.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tree_info.d" -o "tree_info.o" "tree_info.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_lstr.d" -o "main_lstr.o" "main_lstr.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_info.d" -o "seq_info.o" "seq_info.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_lssq.d" -o "main_lssq.o" "main_lssq.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "upgma.d" -o "upgma.o" "upgma.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_upgma.d" -o "main_upgma.o" "main_upgma.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "clsq.d" -o "clsq.o" "clsq.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_clsq.d" -o "main_clsq.o" "main_clsq.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "clean_tree.d" -o "clean_tree.o" "clean_tree.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_cltr.d" -o "main_cltr.o" "main_cltr.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_s2fa.d" -o "main_s2fa.o" "main_s2fa.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_s2phy.d" -o "main_s2phy.o" "main_s2phy.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_fqfilt.d" -o "main_fqfilt.o" "main_fqfilt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_revcomp.d" -o "main_revcomp.o" "main_revcomp.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "edlib.d" -o "edlib.o" "edlib.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_nw.d" -o "main_nw.o" "main_nw.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_sw.d" -o "main_sw.o" "main_sw.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_sample.d" -o "seq_sample.o" "seq_sample.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_boot.d" -o "main_boot.o" "main_boot.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "concat.d" -o "concat.o" "concat.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_concat.d" -o "main_concat.o" "main_concat.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "sstat.d" -o "sstat.o" "sstat.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_sstat.d" -o "main_sstat.o" "main_sstat.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "recode.d" -o "recode.o" "recode.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_recode.d" -o "main_recode.o" "main_recode.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_bp.d" -o "main_bp.o" "main_bp.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_t2new.d" -o "main_t2new.o" "main_t2new.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_t2nex.d" -o "main_t2nex.o" "main_t2nex.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rr.d" -o "main_rr.o" "main_rr.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d" -o "aa2cdn.o" "aa2cdn.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_aa2cdn.d" -o "main_aa2cdn.o" "main_aa2cdn.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tlate.d" -o "tlate.o" "tlate.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_tlate.d" -o "main_tlate.o" "main_tlate.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rms.d" -o "main_rms.o" "main_rms.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rmt.d" -o "main_rmt.o" "main_rmt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_trt.d" -o "main_trt.o" "main_trt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rmk.d" -o "main_rmk.o" "main_rmk.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "nj.d" -o "nj.o" "nj.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_nj.d" -o "main_nj.o" "main_nj.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "log_manip.d" -o "log_manip.o" "log_manip.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_log.d" -o "main_log.o" "main_log.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "vcf_reader.d" -o "vcf_reader.o" "vcf_reader.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_vcf2fa.d" -o "main_vcf2fa.o" "main_vcf2fa.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "relabel.d" -o "relabel.o" "relabel.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rlt.d" -o "main_rlt.o" "main_rlt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rls.d" -o "main_rls.o" "main_rls.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tscale.d" -o "tscale.o" "tscale.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_tscale.d" -o "main_tscale.o" "main_tscale.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "rate_model.d" -o "rate_model.o" "rate_model.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "state_reconstructor.d" -o "state_reconstructor.o" "state_reconstructor.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_nlopt.d" -o "optimize_state_reconstructor_nlopt.o" "optimize_state_reconstructor_nlopt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_periods_nlopt.d" -o "optimize_state_reconstructor_periods_nlopt.o" "optimize_state_reconstructor_periods_nlopt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "branch_segment.d" -o "branch_segment.o" "branch_segment.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "cont_models.d" -o "cont_models.o" "cont_models.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_gen.d" -o "seq_gen.o" "seq_gen.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_strec.d" -o "main_strec.o" "main_strec.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_seqgen.d" -o "main_seqgen.o" "main_seqgen.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_ssort.d" -o "main_ssort.o" "main_ssort.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_contrates.d" -o "main_contrates.o" "main_contrates.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "optimize_cont_models_nlopt.d" -o "optimize_cont_models_nlopt.o" "optimize_cont_models_nlopt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_tcol.d" -o "main_tcol.o" "main_tcol.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_tcomb.d" -o "main_tcomb.o" "main_tcomb.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "collapse_tree.d" -o "collapse_tree.o" "collapse_tree.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_colt.d" -o "main_colt.o" "main_colt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "bd_fit.d" -o "bd_fit.o" "bd_fit.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_bd_fit.d" -o "main_bd_fit.o" "main_bd_fit.cpp" building pxmrca g++ -o "pxmrca" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_mrca.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxmrcacut g++ -o "pxmrcacut" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_mrca_cut.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxmrcaname g++ -o "pxmrcaname" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_mrca_name.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxconsq g++ -o "pxconsq" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_consq.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxbdsim g++ -o "pxbdsim" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize bd_sim.o main_bd_sim.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxlstr g++ -o "pxlstr" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize tree_info.o main_lstr.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o bulding pxlssq g++ -o "pxlssq" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize seq_info.o main_lssq.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxupgma g++ -o "pxupgma" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize upgma.o main_upgma.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxclsq g++ -o "pxclsq" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize clsq.o main_clsq.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxcltr g++ -o "pxcltr" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize clean_tree.o main_cltr.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxs2fa g++ -o "pxs2fa" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2fa.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxs2phy g++ -o "pxs2phy" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2phy.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxs2nex g++ -o "pxs2nex" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2nex.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxfqfilt g++ -o "pxfqfilt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_fqfilt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrevcomp g++ -o "pxrevcomp" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_revcomp.o edlib.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxnw g++ -o "pxnw" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_nw.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxsw g++ -o "pxsw" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_sw.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxboot g++ -o "pxboot" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize seq_sample.o main_boot.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxcat g++ -o "pxcat" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize concat.o main_concat.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxsstat g++ -o "pxsstat" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize sstat.o main_sstat.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrecode g++ -o "pxrecode" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize recode.o main_recode.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxbp g++ -o "pxbp" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_bp.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxt2new g++ -o "pxt2new" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_t2new.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxt2nex g++ -o "pxt2nex" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_t2nex.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrr g++ -o "pxrr" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_rr.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxaa2cdn g++ -o "pxaa2cdn" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize aa2cdn.o main_aa2cdn.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtlate g++ -o "pxtlate" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize tlate.o main_tlate.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrms g++ -o "pxrms" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_rms.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrmt g++ -o "pxrmt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_rmt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtrt g++ -o "pxtrt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_trt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrmk g++ -o "pxrmk" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_rmk.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxnj g++ -o "pxnj" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize nj.o main_nj.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxlog g++ -o "pxlog" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize log_manip.o main_log.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxvcf2fa g++ -o "pxvcf2fa" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize vcf_reader.o main_vcf2fa.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrlt g++ -o "pxrlt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize relabel.o main_rlt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrls g++ -o "pxrls" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize relabel.o main_rls.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtscale g++ -o "pxtscale" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize tscale.o main_tscale.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtcol g++ -o "pxtcol" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_tcol.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtcomb g++ -o "pxtcomb" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_tcomb.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxcolt g++ -o "pxcolt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize collapse_tree.o main_colt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxbdfit g++ -o "pxbdfit" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize bd_fit.o main_bd_fit.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo building pxssort g++ -o "pxssort" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_ssort.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxstrec g++ -o "pxstrec" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_strec.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt # -lgfortran building pxseqgen g++ -o "pxseqgen" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_seqgen.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt building pxcontrates g++ -o "pxcontrates" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_contrates.o optimize_cont_models_nlopt.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt make[1]: Leaving directory '/build/phyx-1.01+ds/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/phyx-1.01+ds' cd src && python3 run_tests.py character: 0 character: 1 character: 2 ================= TESTING pxcontrates PASSED ================= TESTING pxseqgen PASSED ================= TESTING pxstrec PASSED ================= TESTING pxssort PASSED ================= TESTING pxbdfit PASSED ================= TESTING pxcolt PASSED ================= TESTING pxtcomb no test for pxtcomb ================= TESTING pxtcol no test for pxtcol ================= TESTING pxtscale PASSED ================= TESTING pxrls PASSED ================= TESTING pxrlt PASSED ================= TESTING pxvcf2fa PASSED ================= TESTING pxlog PASSED ================= TESTING pxnj PASSED ================= TESTING pxrmk PASSED ================= TESTING pxtrt no test for pxtrt ================= TESTING pxrmt PASSED ================= TESTING pxrms PASSED ================= TESTING pxtlate PASSED ================= TESTING pxaa2cdn PASSED ================= TESTING pxrr PASSED ================= TESTING pxt2nex PASSED ================= TESTING pxt2new PASSED ================= TESTING pxbp PASSED ================= TESTING pxrecode PASSED ================= TESTING pxcat PASSED ================= TESTING pxsstat PASSED ================= TESTING pxboot PASSED ================= TESTING pxsw PASSED ================= TESTING pxnw PASSED ================= TESTING pxrevcomp PASSED ================= TESTING pxfqfilt PASSED ================= TESTING pxs2nex PASSED ================= TESTING pxs2phy PASSED ================= TESTING pxs2fa PASSED ================= TESTING pxcltr no test for pxcltr ================= TESTING pxclsq PASSED ================= TESTING pxupgma PASSED ================= TESTING pxlssq PASSED ================= TESTING pxlstr PASSED ================= TESTING pxbdsim PASSED ================= TESTING pxconsq PASSED ================= TESTING pxmrcaname PASSED ================= TESTING pxmrcacut PASSED ================= TESTING pxmrca PASSED ================= PASSED TESTS: 41 FAILED TESTS: 0 make[1]: Leaving directory '/build/phyx-1.01+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/phyx-1.01+ds' mkdir -p /build/phyx-1.01+ds/debian/phyx/usr/bin dh_auto_install -- prefix=/build/phyx-1.01+ds/debian/phyx/usr cd src && make -j16 install DESTDIR=/build/phyx-1.01\+ds/debian/phyx AM_UPDATE_INFO_DIR=no prefix=/build/phyx-1.01\+ds/debian/phyx/usr make[2]: Entering directory '/build/phyx-1.01+ds/src' install -m 0755 px* /build/phyx-1.01+ds/debian/phyx/usr/bin make[2]: Leaving directory '/build/phyx-1.01+ds/src' #echo "#!/usr/bin/python3" > /build/phyx-1.01+ds/debian/phyx/usr/bin/Phyx_Gui #cat src/Phyx_Gui.py >> /build/phyx-1.01+ds/debian/phyx/usr/bin/Phyx_Gui make[1]: Leaving directory '/build/phyx-1.01+ds' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory '/build/phyx-1.01+ds' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/phyx-1.01+ds' dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'phyx' in '../phyx_1.01+ds-2+deb11u1_amd64.deb'. dpkg-deb: building package 'phyx-dbgsym' in '../phyx-dbgsym_1.01+ds-2+deb11u1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phyx_1.01+ds-2+deb11u1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3403589/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3403589/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3403589 and its subdirectories I: Current time: Sat Jun 1 10:30:16 +14 2024 I: pbuilder-time-stamp: 1717187416