I: pbuilder: network access will be disabled during build I: Current time: Fri May 31 10:02:46 -12 2024 I: pbuilder-time-stamp: 1717192966 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: using eatmydata during job 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.nSvU3oJX/trustedkeys.kbx': General error gpgv: Signature made Sat Feb 4 09:56:08 2023 -12 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/25969/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='f347418171994cbd94d63ae226b94a02' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='25969' 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.abwmsHb3/pbuilderrc_ylDm --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.abwmsHb3/b1 --logfile b1/build.log phyx_1.01+ds-2+deb11u1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jan 20 2022 more -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 May 23 03:56 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/25969/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: i386 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 ... 19727 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 37.0 MB of archives. After unpacking 149 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2+deb11u5 [101 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u4 [728 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 hdf5-helpers i386 1.10.6+repack-4+deb11u1 [40.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libaec0 i386 1.0.4-1 [22.6 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libsz2 i386 1.0.4-1 [6820 B] Get: 47 http://deb.debian.org/debian bullseye/main i386 libaec-dev i386 1.0.4-1 [21.5 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libarpack2 i386 3.8.0-1 [103 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libsuperlu5 i386 5.2.2+dfsg1-2 [161 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libarmadillo10 i386 1:10.1.2+dfsg-6 [103 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libblas-dev i386 3.9.0-3 [157 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 liblapack-dev i386 3.9.0-3 [3759 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libarpack2-dev i386 3.8.0-1 [123 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libhdf5-103-1 i386 1.10.6+repack-4+deb11u1 [1160 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libhdf5-fortran-102 i386 1.10.6+repack-4+deb11u1 [113 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-100 i386 1.10.6+repack-4+deb11u1 [93.2 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-fortran-100 i386 1.10.6+repack-4+deb11u1 [58.6 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libhdf5-cpp-103-1 i386 1.10.6+repack-4+deb11u1 [149 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-cpp-100 i386 1.10.6+repack-4+deb11u1 [38.2 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2+deb11u2 [194 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo-dev i386 1:2.0.6-4 [299 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libjpeg-dev i386 1:2.0.6-4 [67.8 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libhdf5-dev i386 1.10.6+repack-4+deb11u1 [2585 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libsuperlu-dev i386 5.2.2+dfsg1-2 [21.4 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libarmadillo-dev i386 1:10.1.2+dfsg-6 [386 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libnlopt0 i386 2.7.0-4+b2 [170 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libnlopt-dev i386 2.7.0-4+b2 [29.8 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libnlopt-cxx0 i386 2.7.0-4+b2 [199 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libnlopt-cxx-dev i386 2.7.0-4+b2 [14.5 kB] Fetched 37.0 MB in 0s (77.3 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 ... 19727 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_i386.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libexpat1:i386 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 20594 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... 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Setting up libaec0:i386 (1.0.4-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libjpeg62-turbo-dev:i386 (1:2.0.6-4) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libnlopt-cxx0:i386 (2.7.0-4+b2) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libnlopt-dev:i386 (2.7.0-4+b2) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libblas-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libsz2:i386 (1.0.4-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up liblapack3:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libaec-dev:i386 (1.0.4-1) ... Setting up libarpack2:i386 (3.8.0-1) ... Setting up libjpeg-dev:i386 (1:2.0.6-4) ... Setting up libsuperlu5:i386 (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:i386 (2.7.0-4+b2) ... Setting up liblapack-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-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:i386 (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:i386 (1.10.6+repack-4+deb11u1) ... Setting up libsuperlu-dev:i386 (5.2.2+dfsg1-2) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up libhdf5-hl-100:i386 (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) ... Setting up libarpack2-dev:i386 (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:i386 (1.10.6+repack-4+deb11u1) ... Setting up libhdf5-fortran-102:i386 (1.10.6+repack-4+deb11u1) ... Setting up libhdf5-hl-fortran-100:i386 (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/i386-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/i386-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libarmadillo-dev (1:10.1.2+dfsg-6) ... 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: Running cd /build/phyx-1.01+ds/ && 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 > ../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 i386 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=i686-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/i386-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 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 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 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 pxcolt PASSED ================= TESTING pxt2nex PASSED ================= TESTING pxcat PASSED ================= TESTING pxrls PASSED ================= TESTING pxs2fa PASSED ================= TESTING pxconsq PASSED ================= TESTING pxrmt PASSED ================= TESTING pxrmk PASSED ================= TESTING pxs2nex PASSED ================= TESTING pxboot PASSED ================= TESTING pxrevcomp PASSED ================= TESTING pxnw PASSED ================= TESTING pxvcf2fa PASSED ================= TESTING pxbp PASSED ================= TESTING pxssort PASSED ================= TESTING pxupgma PASSED ================= TESTING pxmrca PASSED ================= TESTING pxrecode PASSED ================= TESTING pxlssq PASSED ================= TESTING pxsw PASSED ================= TESTING pxtcomb no test for pxtcomb ================= TESTING pxbdsim PASSED ================= TESTING pxfqfilt PASSED ================= TESTING pxmrcacut PASSED ================= TESTING pxtscale PASSED ================= TESTING pxlstr PASSED ================= TESTING pxnj PASSED ================= TESTING pxs2phy PASSED ================= TESTING pxaa2cdn PASSED ================= TESTING pxrms PASSED ================= TESTING pxrr PASSED ================= TESTING pxrlt PASSED ================= TESTING pxbdfit PASSED ================= TESTING pxseqgen PASSED ================= TESTING pxclsq PASSED ================= TESTING pxsstat PASSED ================= TESTING pxtlate PASSED ================= TESTING pxt2new PASSED ================= TESTING pxtrt no test for pxtrt ================= TESTING pxcontrates PASSED ================= TESTING pxtcol no test for pxtcol ================= TESTING pxmrcaname PASSED ================= TESTING pxlog PASSED ================= TESTING pxstrec n 0 False a . False n 3 False 1 False 6 False FAILED intended output: 0.316161 your output: nan ================= TESTING pxcltr no test for pxcltr ================= PASSED TESTS: 40 FAILED TESTS: 1 These failed: pxstrec 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_i386.deb'. dpkg-deb: building package 'phyx-dbgsym' in '../phyx-dbgsym_1.01+ds-2+deb11u1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phyx_1.01+ds-2+deb11u1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/25969 and its subdirectories I: Current time: Fri May 31 10:03:39 -12 2024 I: pbuilder-time-stamp: 1717193019