I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 8 08:24:14 -12 2024 I: pbuilder-time-stamp: 1731097454 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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_1.3.2+ds-1.dsc] I: copying [./phyx_1.3.2+ds.orig.tar.xz] I: copying [./phyx_1.3.2+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 2 15:52:47 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phyx_1.3.2+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting phyx in phyx-1.3.2+ds dpkg-source: info: unpacking phyx_1.3.2+ds.orig.tar.xz dpkg-source: info: unpacking phyx_1.3.2+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying build-more-programs.patch dpkg-source: info: applying whatis.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3574295/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='389352b0cdf54e0bb8246643ac561c60' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3574295' 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.eB9m86lU/pbuilderrc_GJgq --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eB9m86lU/b1 --logfile b1/build.log phyx_1.3.2+ds-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3574295/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3:any, 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 ... 19970 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3:any. 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} libarmadillo14{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libnsl2{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsuperlu-dev{a} libsuperlu6{a} libsuperlu7{a} libsz2{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 113 newly installed, 0 to remove and 0 not upgraded. Need to get 54.6 MB of archives. After unpacking 216 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-2 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-2 [2161 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-2 [1967 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-2 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-10 [97.2 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.10.10+repack-4 [23.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 55 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libarpack2t64 amd64 3.9.1-1.1+b2 [104 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libsuperlu6 amd64 6.0.1+dfsg1-1+b1 [170 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libarmadillo14 amd64 1:14.0.1+dfsg-2 [102 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3+b1 [161 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3+b1 [4990 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libarpack2-dev amd64 3.9.1-1.1+b2 [119 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.10.1-2 [352 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4 [1253 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-4 [89.5 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4 [63.9 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-4 [40.5 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-4 [130 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-4 [21.4 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b5 [316 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b2 [642 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.6-2+b1 [439 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2+b1 [439 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.6-2+b1 [1385 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libcurl4-openssl-dev amd64 8.10.1-2 [462 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.10.10+repack-4 [2652 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libsuperlu7 amd64 7.0.0+dfsg1-2 [174 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libsuperlu-dev amd64 7.0.0+dfsg1-2 [21.9 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libarmadillo-dev amd64 1:14.0.1+dfsg-2 [412 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-5+b5 [178 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libnlopt-dev amd64 2.7.1-5+b5 [46.8 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx0 amd64 2.7.1-5+b5 [205 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx-dev amd64 2.7.1-5+b5 [13.4 kB] Fetched 54.6 MB in 3s (18.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. 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Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgnutls-openssl27t64:amd64 (3.8.6-2+b1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-10) ... Setting up hdf5-helpers (1.10.10+repack-4) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b5) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libnlopt0:amd64 (2.7.1-5+b5) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Nov 8 20:26:42 UTC 2024. Universal Time is now: Fri Nov 8 20:26:42 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3+b1) ... 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 libunbound8:amd64 (1.22.0-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2+b1) ... 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Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-4) ... Setting up python3 (3.12.6-1) ... Setting up libhdf5-dev (1.10.10+repack-4) ... 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 (1:14.0.1+dfsg-2) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/phyx-1.3.2+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_1.3.2+ds-1_source.changes dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 1.3.2+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds' rm -rf src/phyx.logfile if [ -r src/Makefile ]; then \ /usr/bin/make -C src distclean; \ fi make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+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 the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for fabs in -lm... yes checking for nlopt_version in -lnlopt... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for nlopt.h... yes checking for library containing wrapper_sgesv_... -larmadillo checking for fenv.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for size_t... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu 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 -j20 make[1]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds/src' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "citations.d" -o "citations.o" "citations.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "log.d" -o "log.o" "log.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "superdouble.d" -o "superdouble.o" "superdouble.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "timer.d" -o "timer.o" "timer.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "sequence.d" -o "sequence.o" "sequence.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_reader.d" -o "seq_reader.o" "seq_reader.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_utils.d" -o "seq_utils.o" "seq_utils.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_models.d" -o "seq_models.o" "seq_models.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "pairwise_alignment.d" -o "pairwise_alignment.o" "pairwise_alignment.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d" -o "aa2cdn.o" "aa2cdn.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_aa2cdn.d" -o "main_aa2cdn.o" "main_aa2cdn.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "node.d" -o "node.o" "node.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tree.d" -o "tree.o" "tree.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tree_reader.d" -o "tree_reader.o" "tree_reader.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tree_utils.d" -o "tree_utils.o" "tree_utils.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "bd_sim.d" -o "bd_sim.o" "bd_sim.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_bd_sim.d" -o "main_bd_sim.o" "main_bd_sim.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_sample.d" -o "seq_sample.o" "seq_sample.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_boot.d" -o "main_boot.o" "main_boot.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_bp.d" -o "main_bp.o" "main_bp.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "concat.d" -o "concat.o" "concat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_cat.d" -o "main_cat.o" "main_cat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "clean_seq.d" -o "clean_seq.o" "clean_seq.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_clsq.d" -o "main_clsq.o" "main_clsq.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "clean_tree.d" -o "clean_tree.o" "clean_tree.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_cltr.d" -o "main_cltr.o" "main_cltr.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "collapse_tree.d" -o "collapse_tree.o" "collapse_tree.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_colt.d" -o "main_colt.o" "main_colt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "comp_test.d" -o "comp_test.o" "comp_test.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_comp.d" -o "main_comp.o" "main_comp.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_consq.d" -o "main_consq.o" "main_consq.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_fqfilt.d" -o "main_fqfilt.o" "main_fqfilt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "log_manip.d" -o "log_manip.o" "log_manip.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_log.d" -o "main_log.o" "main_log.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_info.d" -o "seq_info.o" "seq_info.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_lssq.d" -o "main_lssq.o" "main_lssq.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tree_info.d" -o "tree_info.o" "tree_info.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_lstr.d" -o "main_lstr.o" "main_lstr.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_mono.d" -o "main_mono.o" "main_mono.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_mrca.d" -o "main_mrca.o" "main_mrca.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_mrca_cut.d" -o "main_mrca_cut.o" "main_mrca_cut.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_mrca_name.d" -o "main_mrca_name.o" "main_mrca_name.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_nw.d" -o "main_nw.o" "main_nw.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "polytomy.d" -o "polytomy.o" "polytomy.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_poly.d" -o "main_poly.o" "main_poly.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "recode.d" -o "recode.o" "recode.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_recode.d" -o "main_recode.o" "main_recode.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_revcomp.d" -o "main_revcomp.o" "main_revcomp.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "edlib.d" -o "edlib.o" "edlib.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "relabel.d" -o "relabel.o" "relabel.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rls.d" -o "main_rls.o" "main_rls.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "upgma.d" -o "upgma.o" "upgma.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_upgma.d" -o "main_upgma.o" "main_upgma.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rlt.d" -o "main_rlt.o" "main_rlt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "nj.d" -o "nj.o" "nj.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_nj.d" -o "main_nj.o" "main_nj.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rmk.d" -o "main_rmk.o" "main_rmk.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rms.d" -o "main_rms.o" "main_rms.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rmt.d" -o "main_rmt.o" "main_rmt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rr.d" -o "main_rr.o" "main_rr.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_s2fa.d" -o "main_s2fa.o" "main_s2fa.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_s2phy.d" -o "main_s2phy.o" "main_s2phy.cpp" nj.cpp: In member function ‘void NJOI::CalcQ(const int&, std::vector >&, std::vector >&, std::vector >&)’: nj.cpp:69:25: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = multiplies; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 69 | std::bind1st(std::multiplies(), static_cast(NumbOfSequences - 2))); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435, from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from nj.cpp:1: /usr/include/c++/14/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "rate_model.d" -o "rate_model.o" "rate_model.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "state_reconstructor.d" -o "state_reconstructor.o" "state_reconstructor.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_nlopt.d" -o "optimize_state_reconstructor_nlopt.o" "optimize_state_reconstructor_nlopt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "branch_segment.d" -o "branch_segment.o" "branch_segment.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "cont_models.d" -o "cont_models.o" "cont_models.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_gen.d" -o "seq_gen.o" "seq_gen.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_seqgen.d" -o "main_seqgen.o" "main_seqgen.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_ssort.d" -o "main_ssort.o" "main_ssort.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "sstat.d" -o "sstat.o" "sstat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_sstat.d" -o "main_sstat.o" "main_sstat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_sw.d" -o "main_sw.o" "main_sw.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_t2new.d" -o "main_t2new.o" "main_t2new.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_t2nex.d" -o "main_t2nex.o" "main_t2nex.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tcol.d" -o "main_tcol.o" "main_tcol.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tcomb.d" -o "main_tcomb.o" "main_tcomb.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tgen.d" -o "tgen.o" "tgen.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tgen.d" -o "main_tgen.o" "main_tgen.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tlate.d" -o "tlate.o" "tlate.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tlate.d" -o "main_tlate.o" "main_tlate.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_trt.d" -o "main_trt.o" "main_trt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tscale.d" -o "tscale.o" "tscale.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tscale.d" -o "main_tscale.o" "main_tscale.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "vcf_reader.d" -o "vcf_reader.o" "vcf_reader.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_vcf2fa.d" -o "main_vcf2fa.o" "main_vcf2fa.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "bd_fit.d" -o "bd_fit.o" "bd_fit.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_bd_fit.d" -o "main_bd_fit.o" "main_bd_fit.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_contrates.d" -o "main_contrates.o" "main_contrates.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "optimize_cont_models_nlopt.d" -o "optimize_cont_models_nlopt.o" "optimize_cont_models_nlopt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_strec.d" -o "main_strec.o" "main_strec.cpp" building pxaa2cdn g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxaa2cdn" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize aa2cdn.o main_aa2cdn.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o building pxbdsim g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxbdsim" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize bd_sim.o main_bd_sim.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxboot building pxbp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxboot" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize seq_sample.o main_boot.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxbp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_bp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxcat g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxcat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize concat.o main_cat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o building pxclsq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxclsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize clean_seq.o main_clsq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o building pxcltr building pxcolt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxcltr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize clean_tree.o main_cltr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxcolt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize collapse_tree.o main_colt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxcomp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize comp_test.o main_comp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxboot.1.in > man/pxboot.1 building pxconsq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxconsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_consq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxbdsim.1.in > man/pxbdsim.1 cat man/pxaa2cdn.1.in > man/pxaa2cdn.1 cat man/pxcltr.1.in > man/pxcltr.1 building pxfqfilt building pxlog g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxfqfilt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_fqfilt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxlog" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize log_manip.o main_log.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxclsq.1.in > man/pxclsq.1 bulding pxlssq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxlssq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize seq_info.o main_lssq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxcolt.1.in > man/pxcolt.1 building pxlstr building pxmono g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxlstr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tree_info.o main_lstr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxmono" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mono.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxconsq.1.in > man/pxconsq.1 building pxmrca g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxmrca" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxcat.1.in > man/pxcat.1 cat man/pxbp.1.in > man/pxbp.1 cat man/pxcomp.1.in > man/pxcomp.1 building pxmrcacut g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxmrcacut" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca_cut.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxmrcaname g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxmrcaname" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca_name.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxnw g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxnw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_nw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxfqfilt.1.in > man/pxfqfilt.1 building pxpoly g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxpoly" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize polytomy.o main_poly.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxmrcacut.1.in > man/pxmrcacut.1 building pxrevcomp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxrevcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_revcomp.o edlib.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxmono.1.in > man/pxmono.1 building pxupgma cat man/pxlog.1.in > man/pxlog.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxupgma" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize upgma.o main_upgma.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxnj g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxnj" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize nj.o main_nj.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxlssq.1.in > man/pxlssq.1 building pxrmk g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxrmk" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rmk.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxlstr.1.in > man/pxlstr.1 cat man/pxmrca.1.in > man/pxmrca.1 building pxrmt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxrmt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rmt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxrr g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxrr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxnw.1.in > man/pxnw.1 building pxs2fa g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxs2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxmrcaname.1.in > man/pxmrcaname.1 building pxs2nex g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxs2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrevcomp.1.in > man/pxrevcomp.1 building pxs2phy g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxs2phy" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2phy.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrmk.1.in > man/pxrmk.1 building pxsstat g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxsstat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize sstat.o main_sstat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrr.1.in > man/pxrr.1 building pxsw cat man/pxs2phy.1.in > man/pxs2phy.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxsw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_sw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o building pxt2new g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxt2new" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_t2new.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxpoly.1.in > man/pxpoly.1 cat man/pxupgma.1.in > man/pxupgma.1 cat man/pxnj.1.in > man/pxnj.1 building pxt2nex g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxt2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_t2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxtcol building pxtcomb g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxtcol" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_tcol.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxtcomb" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_tcomb.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxs2fa.1.in > man/pxs2fa.1 building pxtgen g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxtgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tgen.o main_tgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxs2nex.1.in > man/pxs2nex.1 building pxtlate g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxtlate" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tlate.o main_tlate.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrmt.1.in > man/pxrmt.1 building pxtrt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxtrt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_trt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxt2new.1.in > man/pxt2new.1 building pxtscale g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxtscale" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tscale.o main_tscale.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxsstat.1.in > man/pxsstat.1 building pxvcf2fa g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxvcf2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize vcf_reader.o main_vcf2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxtlate.1.in > man/pxtlate.1 building pxbdfit g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o "pxbdfit" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize bd_fit.o main_bd_fit.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxtcol.1.in > man/pxtcol.1 cat man/pxsw.1.in > man/pxsw.1 cat man/pxt2nex.1.in > man/pxt2nex.1 cat man/pxtcomb.1.in > man/pxtcomb.1 cat man/pxtrt.1.in > man/pxtrt.1 cat man/pxvcf2fa.1.in > man/pxvcf2fa.1 cat man/pxtgen.1.in > man/pxtgen.1 cat man/pxbdfit.1.in > man/pxbdfit.1 cat man/pxtscale.1.in > man/pxtscale.1 building pxrecode g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxrecode" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize recode.o main_recode.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrecode.1.in > man/pxrecode.1 building pxrms g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxrms" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rms.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrms.1.in > man/pxrms.1 building pxssort g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxssort" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_ssort.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o building pxrls g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxrls" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize relabel.o main_rls.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxrlt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o "pxrlt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize relabel.o main_rlt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxssort.1.in > man/pxssort.1 cat man/pxrls.1.in > man/pxrls.1 cat man/pxrlt.1.in > man/pxrlt.1 building pxseqgen g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o "pxseqgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_seqgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.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 -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo building pxcontrates g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o "pxcontrates" -O3 -std=c++14 -fopenmp -Wall -DOMP -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 ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxseqgen.1.in > man/pxseqgen.1 cat man/pxcontrates.1.in > man/pxcontrates.1 building pxstrec g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o "pxstrec" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_strec.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.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 -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo # -lgfortran cat man/pxstrec.1.in > man/pxstrec.1 make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds' cd src && python3 run_tests.py character: 0 character: 1 character: 2 ================= TESTING pxaa2cdn aa2cdn PASSED aa2cdn (remove last codon, all) PASSED aa2cdn (remove stop codon, mixed) PASSED PASSED ================= TESTING pxbdfit yule PASSED birth-death PASSED best PASSED PASSED ================= TESTING pxbdsim taxon stop PASSED time stop PASSED PASSED ================= TESTING pxboot bootstrap PASSED jackknife PASSED PASSED ================= TESTING pxbp node-based PASSED edge-based PASSED PASSED ================= TESTING pxcat PASSED ================= TESTING pxclsq delete proportion PASSED remove empty PASSED min 4 chars per site PASSED info by taxon PASSED PASSED ================= TESTING pxcltr all PASSED labels PASSED knuckles PASSED PASSED ================= TESTING pxcolt probability support PASSED integer support PASSED real support PASSED PASSED ================= TESTING pxcomp PASSED ================= TESTING pxconsq PASSED ================= TESTING pxcontrates PASSED ================= TESTING pxfqfilt PASSED ================= TESTING pxlog count trees PASSED tree log PASSED count parameters PASSED parameter log PASSED summarize parameters PASSED PASSED ================= TESTING pxlssq default PASSED labels PASSED frequencies PASSED indidivual stats PASSED binary data PASSED morph data PASSED fastq PASSED unaliagned PASSED individual missing PASSED PASSED ================= TESTING pxlstr newick PASSED nexus (mulitple) PASSED figtree PASSED polytomy PASSED internal linebreak PASSED terminal labels PASSED PASSED ================= TESTING pxmono PASSED ================= TESTING pxmrca PASSED ================= TESTING pxmrcacut PASSED ================= TESTING pxmrcaname PASSED ================= TESTING pxnj PASSED ================= TESTING pxnw PASSED ================= TESTING pxpoly PASSED ================= TESTING pxrecode RY-coding PASSED MK-coding PASSED SW-coding PASSED PASSED ================= TESTING pxrevcomp PASSED ================= TESTING pxrls name files PASSED regex PASSED ================= TESTING pxrlt name files PASSED regex PASSED ================= TESTING pxrmk PASSED ================= TESTING pxrms command line arg PASSED regex PASSED PASSED ================= TESTING pxrmt command line arg PASSED regex PASSED PASSED ================= TESTING pxrr PASSED ================= TESTING pxs2fa nexus PASSED interleaved nexus PASSED phylip PASSED interleaved phylip PASSED fastq PASSED PASSED ================= TESTING pxs2nex fasta PASSED phylip PASSED interleaved phylip PASSED interleaved nexus PASSED fastq PASSED PASSED ================= TESTING pxs2phy fasta PASSED nexus PASSED interleaved nexus PASSED interleaved phylip PASSED PASSED ================= TESTING pxseqgen PASSED ================= TESTING pxssort sort by id PASSED sort by id rev PASSED sort by length (<) PASSED sort by length (>) PASSED PASSED ================= TESTING pxsstat PASSED ================= TESTING pxstrec PASSED ================= TESTING pxsw PASSED ================= TESTING pxt2new PASSED ================= TESTING pxt2nex PASSED ================= TESTING pxtcol no test for pxtcol ================= TESTING pxtcomb no test for pxtcomb ================= TESTING pxtgen unrooted PASSED rooted PASSED prefix label PASSED PASSED ================= TESTING pxtlate standard PASSED vert mtDNA PASSED PASSED ================= TESTING pxtrt PASSED ================= TESTING pxtscale scale PASSED root height PASSED PASSED ================= TESTING pxupgma PASSED ================= TESTING pxvcf2fa PASSED ================= PASSED PROGRAMS: 47 (102 tests) FAILED PROGRAMS: 0 (0 tests) PROGRAMS WITHOUT TESTS: 2 make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+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/reproducible-path/phyx-1.3.2+ds' mkdir -p /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin dh_auto_install -- PREFIX=/build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr cd src && make -j20 install DESTDIR=/build/reproducible-path/phyx-1.3.2\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/build/reproducible-path/phyx-1.3.2\+ds/debian/phyx/usr make[2]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds/src' mkdir -p /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin && install -m 0755 px* /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin mkdir -p /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/share/man/man1 && install -m 0755 man/px*.1 /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds/src' #echo "#!/usr/bin/python3" > /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin/Phyx_Gui #cat src/Phyx_Gui.py >> /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin/Phyx_Gui make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -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/reproducible-path/phyx-1.3.2+ds' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds' dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'phyx' in '../phyx_1.3.2+ds-1_amd64.deb'. dpkg-deb: building package 'phyx-dbgsym' in '../phyx-dbgsym_1.3.2+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../phyx_1.3.2+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../phyx_1.3.2+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3574295 and its subdirectories I: Current time: Fri Nov 8 08:32:17 -12 2024 I: pbuilder-time-stamp: 1731097937