Wed May 8 05:04:20 UTC 2024 I: starting to build phyx/trixie/amd64 on jenkins on '2024-05-08 05:04' Wed May 8 05:04:20 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_37/10337/console.log Wed May 8 05:04:20 UTC 2024 I: Downloading source for trixie/phyx=1.3.1+ds-2 --2024-05-08 05:04:21-- http://deb.debian.org/debian/pool/main/p/phyx/phyx_1.3.1%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2173 (2.1K) [text/prs.lines.tag] Saving to: ‘phyx_1.3.1+ds-2.dsc’ 0K .. 100% 270M=0s 2024-05-08 05:04:21 (270 MB/s) - ‘phyx_1.3.1+ds-2.dsc’ saved [2173/2173] Wed May 8 05:04:21 UTC 2024 I: phyx_1.3.1+ds-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phyx Binary: phyx Architecture: any Version: 1.3.1+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/FePhyFoFum/phyx Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/phyx Vcs-Git: https://salsa.debian.org/med-team/phyx.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libarmadillo-dev Package-List: phyx deb science optional arch=any Checksums-Sha1: b91fef57e035c34bf92fedc8d7dbc8cad0fbed0c 1191388 phyx_1.3.1+ds.orig.tar.xz 47f5caaab67ac5939c81e3ba8ce17a45b3102f27 10676 phyx_1.3.1+ds-2.debian.tar.xz Checksums-Sha256: ab788a470997954c3cec6a4b60d2d131ca3f129a3f8946f4b63041abeba35b53 1191388 phyx_1.3.1+ds.orig.tar.xz c70bff20e192bf59a17c6676e66746230841556d14840adb6fd6d5dc761b8e86 10676 phyx_1.3.1+ds-2.debian.tar.xz Files: 874ffc6583f2de805514029b216d75a6 1191388 phyx_1.3.1+ds.orig.tar.xz 261dd292d0eab7550a9829ece1683d94 10676 phyx_1.3.1+ds-2.debian.tar.xz Dgit: af90e03dfc8a805b7b243d11d9cf038a09f1cf7c debian archive/debian/1.3.1+ds-2 https://git.dgit.debian.org/phyx -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmTbP4IUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp5VA//a90vGQgJtRYYDE8UylVi3zXntmWm ErtPyfaaYKvXPlfpmof+DtlNFs8atueVOffNKBmlUSNgNsJ8greiZ6/wmk36//bI aDz6T1c6T6m+u6TKYqR/J7ls9FWZ6yi0OvHXnjH+KYRwqD1wSa0yW06/73F8LR/z 0YeQpKVXh+fZxlJ0RUQkjsGvoZfkJ/jtokIHPPfu4uAtCPQxVBzLb5AUPzix87L5 E9u2lFd6avhyByaQq5FfvGhAAaOAZvJfK2ukIdxVIkIUh7Ddj1CK64XHVFLBKxjU F1tqmVqa9LI2x+Sgsjo8J+737cj43RjjgBQdAJ6KlVdCOldq89T8MthyagzavBlB pf9NdofpvgaB49WgyK5ZFg7ZMzGqHUT6mT2baP/r8SXu+ErBZBDFIMW9PibDFUkb +APl8r7y0gOFx4Y6odO2auSBJkydfyLzsAEQnv6vGkZFSFpQO7AuchJGnCsY0/HC UZ3DBrVdSXfdzEgkpE5jQSBPnoQS/nhVqU1P/y5yoStQXhBt9+6gUvV2CbeyWbpA CqksLesgfORvtszXOk7jtH+GUIMlptNAjtrPqQzQYPISW+Jfax1YdOkwaIUePWYy CKDSaJB6ja76W3fkp/LInZJ91PYdxBWk4bLOBLkZIi/5/1nKMdyKo2zyaZ2PD1D5 3Pf30D5JNsEBxGw= =jXZl -----END PGP SIGNATURE----- Wed May 8 05:04:21 UTC 2024 I: Checking whether the package is not for us Wed May 8 05:04:21 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Wed May 8 05:04:21 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Wed May 8 05:07:43 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 7 17:04:23 -12 2024 I: pbuilder-time-stamp: 1715144663 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [phyx_1.3.1+ds-2.dsc] I: copying [./phyx_1.3.1+ds.orig.tar.xz] I: copying [./phyx_1.3.1+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Aug 15 09:04:02 2023 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_1.3.1+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting phyx in phyx-1.3.1+ds dpkg-source: info: unpacking phyx_1.3.1+ds.orig.tar.xz dpkg-source: info: unpacking phyx_1.3.1+ds-2.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 i386.patch dpkg-source: info: applying deoptimize.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/1524522/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=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b6a9e41fd0c44e4a8e89df64da7e37f3' 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='1524522' 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.ornYqdEU/pbuilderrc_FRl3 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ornYqdEU/b1 --logfile b1/build.log phyx_1.3.1+ds-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1524522/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, 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 ... 19698 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; 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} libarmadillo12{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{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} 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} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssl-dev{a} libsub-override-perl{a} libsuperlu-dev{a} libsuperlu6{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-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 lynx publicsuffix wget 0 packages upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 45.6 MB of archives. After unpacking 191 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 hdf5-helpers amd64 1.10.10+repack-3.3 [23.4 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 47 http://deb.debian.org/debian trixie/main amd64 libaec-dev amd64 1.1.3-1 [21.0 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libarpack2t64 amd64 3.9.1-1.1+b1 [104 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libsuperlu6 amd64 6.0.1+dfsg1-1+b1 [170 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libarmadillo12 amd64 1:12.6.7+dfsg-1 [102 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libarpack2-dev amd64 3.9.1-1.1+b1 [119 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 62 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-3 [441 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-3.3 [89.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-3.3 [40.4 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.3 [131 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-3.3 [21.3 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libcurl4-openssl-dev amd64 8.7.1-3 [547 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.10.10+repack-3.3 [2639 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libsuperlu-dev amd64 6.0.1+dfsg1-1+b1 [21.8 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libarmadillo-dev amd64 1:12.6.7+dfsg-1 [408 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libnlopt0 amd64 2.7.1-5+b2 [174 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libnlopt-dev amd64 2.7.1-5+b2 [46.8 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libnlopt-cxx0 amd64 2.7.1-5+b2 [201 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libnlopt-cxx-dev amd64 2.7.1-5+b2 [13.4 kB] Fetched 45.6 MB in 1s (58.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/phyx-1.3.1+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_1.3.1+ds-2_source.changes dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 1.3.1+ds-2 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-1.3.1+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-1.3.1+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... 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 -j12 make[1]: Entering directory '/build/reproducible-path/phyx-1.3.1+ds/src' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "citations.d" -o "citations.o" "citations.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "log.d" -o "log.o" "log.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "superdouble.d" -o "superdouble.o" "superdouble.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "timer.d" -o "timer.o" "timer.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "sequence.d" -o "sequence.o" "sequence.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d" -o "aa2cdn.o" "aa2cdn.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "node.d" -o "node.o" "node.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree.d" -o "tree.o" "tree.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_reader.d" -o "tree_reader.o" "tree_reader.cpp" utils.cpp: In function ‘void v_mean_variance(std::vector&, double&, double&)’: utils.cpp:457:21: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 457 | std::bind2nd(std::minus(), mn)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_utils.d" -o "tree_utils.o" "tree_utils.cpp" In file included from /usr/include/c++/13/bits/stl_function.h:1438, from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from utils.cpp:1: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ utils.cpp: In function ‘double v_variance(std::vector&)’: utils.cpp:468:21: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 468 | std::bind2nd(std::minus(), meann)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ utils.cpp: In function ‘std::vector average_vectors_elementwise(std::vector&, std::vector&)’: utils.cpp:543:69: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = multiplies; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 543 | std::transform(res.begin(), res.end(), res.begin(), std::bind1st(std::multiplies(), 0.5)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "concat.d" -o "concat.o" "concat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "polytomy.d" -o "polytomy.o" "polytomy.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "recode.d" -o "recode.o" "recode.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "edlib.d" -o "edlib.o" "edlib.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "relabel.d" -o "relabel.o" "relabel.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "upgma.d" -o "upgma.o" "upgma.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "nj.d" -o "nj.o" "nj.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rmt.d" -o "main_rmt.o" "main_rmt.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++/13/bits/stl_function.h:1438, from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from nj.cpp:1: /usr/include/c++/13/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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2phy.d" -o "main_s2phy.o" "main_s2phy.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "sstat.d" -o "sstat.o" "sstat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tgen.d" -o "tgen.o" "tgen.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tlate.d" -o "tlate.o" "tlate.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tscale.d" -o "tscale.o" "tscale.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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 -Wl,-z,relro -Wl,-z,now -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-1.3.1+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-1.3.1+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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxbp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 cat man/pxbdsim.1.in > man/pxbdsim.1 cat man/pxboot.1.in > man/pxboot.1 cat man/pxaa2cdn.1.in > man/pxaa2cdn.1 building pxcat building pxclsq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 cat man/pxbp.1.in > man/pxbp.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxcolt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 cat man/pxcat.1.in > man/pxcat.1 cat man/pxclsq.1.in > man/pxclsq.1 building pxcomp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxconsq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxcltr.1.in > man/pxcltr.1 building pxfqfilt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 cat man/pxcolt.1.in > man/pxcolt.1 building pxlog bulding pxlssq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxcomp.1.in > man/pxcomp.1 building pxlstr g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 cat man/pxconsq.1.in > man/pxconsq.1 building pxmono g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxfqfilt.1.in > man/pxfqfilt.1 building pxmrca g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxlssq.1.in > man/pxlssq.1 cat man/pxlog.1.in > man/pxlog.1 building pxmrcacut building pxmrcaname g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxpoly cat man/pxlstr.1.in > man/pxlstr.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxrecode g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxrevcomp cat man/pxmrca.1.in > man/pxmrca.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 pxrls g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 pxupgma cat man/pxmrcaname.1.in > man/pxmrcaname.1 cat man/pxmrcacut.1.in > man/pxmrcacut.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 pxrlt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxnj g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxnw.1.in > man/pxnw.1 building pxrmk cat man/pxrevcomp.1.in > man/pxrevcomp.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxpoly.1.in > man/pxpoly.1 building pxrms g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxrmt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 cat man/pxrls.1.in > man/pxrls.1 cat man/pxrecode.1.in > man/pxrecode.1 building pxrr g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxs2fa cat man/pxupgma.1.in > man/pxupgma.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxs2nex g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxnj.1.in > man/pxnj.1 cat man/pxrmk.1.in > man/pxrmk.1 cat man/pxrms.1.in > man/pxrms.1 cat man/pxrmt.1.in > man/pxrmt.1 building pxs2phy building pxssort cat man/pxrlt.1.in > man/pxrlt.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 cat man/pxrr.1.in > man/pxrr.1 building pxsstat building pxsw cat man/pxs2fa.1.in > man/pxs2fa.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxt2nex g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxs2nex.1.in > man/pxs2nex.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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-1.3.1+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 cat man/pxsstat.1.in > man/pxsstat.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxtgen g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxssort.1.in > man/pxssort.1 cat man/pxs2phy.1.in > man/pxs2phy.1 building pxtlate g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxsw.1.in > man/pxsw.1 building pxtrt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 building pxtscale g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxt2nex.1.in > man/pxt2nex.1 cat man/pxt2new.1.in > man/pxt2new.1 cat man/pxtcol.1.in > man/pxtcol.1 cat man/pxtcomb.1.in > man/pxtcomb.1 building pxvcf2fa building pxbdfit g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxtgen.1.in > man/pxtgen.1 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxtlate.1.in > man/pxtlate.1 cat man/pxtscale.1.in > man/pxtscale.1 cat man/pxtrt.1.in > man/pxtrt.1 cat man/pxvcf2fa.1.in > man/pxvcf2fa.1 cat man/pxbdfit.1.in > man/pxbdfit.1 building pxseqgen g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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 cat man/pxseqgen.1.in > man/pxseqgen.1 building pxcontrates g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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/pxcontrates.1.in > man/pxcontrates.1 building pxstrec g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.1+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-1.3.1+ds/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/phyx-1.3.1+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 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 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 (100 tests) FAILED PROGRAMS: 0 (0 tests) PROGRAMS WITHOUT TESTS: 2 make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.1+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-1.3.1+ds' mkdir -p /build/reproducible-path/phyx-1.3.1+ds/debian/phyx/usr/bin dh_auto_install -- PREFIX=/build/reproducible-path/phyx-1.3.1+ds/debian/phyx/usr cd src && make -j12 install DESTDIR=/build/reproducible-path/phyx-1.3.1\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/build/reproducible-path/phyx-1.3.1\+ds/debian/phyx/usr make[2]: Entering directory '/build/reproducible-path/phyx-1.3.1+ds/src' mkdir -p /build/reproducible-path/phyx-1.3.1+ds/debian/phyx/usr/bin && install -m 0755 px* /build/reproducible-path/phyx-1.3.1+ds/debian/phyx/usr/bin mkdir -p /build/reproducible-path/phyx-1.3.1+ds/debian/phyx/usr/share/man/man1 && install -m 0755 man/px*.1 /build/reproducible-path/phyx-1.3.1+ds/debian/phyx/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/phyx-1.3.1+ds/src' #echo "#!/usr/bin/python3" > /build/reproducible-path/phyx-1.3.1+ds/debian/phyx/usr/bin/Phyx_Gui #cat src/Phyx_Gui.py >> /build/reproducible-path/phyx-1.3.1+ds/debian/phyx/usr/bin/Phyx_Gui make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.1+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-1.3.1+ds' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.1+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-dbgsym' in '../phyx-dbgsym_1.3.1+ds-2_amd64.deb'. dpkg-deb: building package 'phyx' in '../phyx_1.3.1+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../phyx_1.3.1+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../phyx_1.3.1+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/1524522 and its subdirectories I: Current time: Tue May 7 17:07:41 -12 2024 I: pbuilder-time-stamp: 1715144861 Wed May 8 05:07:43 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Wed May 8 05:07:43 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Wed May 8 05:10:54 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Wed May 8 05:10:55 UTC 2024 I: phyx_1.3.1+ds-2_amd64.changes: Format: 1.8 Date: Tue, 15 Aug 2023 10:45:37 +0200 Source: phyx Binary: phyx phyx-dbgsym Architecture: amd64 Version: 1.3.1+ds-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: phyx - UNIX-style phylogenetic analyses on trees and sequences Closes: 1044139 Changes: phyx (1.3.1+ds-2) unstable; urgency=medium . * d/rules: build with -ffunction-sections on hppa. Thanks to John David Anglin (Closes: #1044139) * d/control: add myself to uploaders. * whatis.patch: new: give meaningful manual pages descriptions. * hardening.patch: new: propagate hardening flags. * d/lintian-overrides: hide hardening no fortifiable information. Some programs part of the phyx distribution do not seem fortifiable at all in spite of the propagation of the appropriate preprocessor flags. Checksums-Sha1: 9632b3c607fa33ea81fcefc92018c16870a08fae 74132912 phyx-dbgsym_1.3.1+ds-2_amd64.deb f181e449254a91ac270b485b5d4c79ffc63646fc 7313 phyx_1.3.1+ds-2_amd64.buildinfo 7c7daa7bfafcaa50ab71f5eb8c9c696e8198518d 2277892 phyx_1.3.1+ds-2_amd64.deb Checksums-Sha256: c7271f5fd7ad1a40df2950fcab9bad8c906f9e0691dd5796c350ded21b98e1a1 74132912 phyx-dbgsym_1.3.1+ds-2_amd64.deb e32cb826693be701aa58ba7fc1b8de24553a5d369c946144e7fd4e7e99b3b6f9 7313 phyx_1.3.1+ds-2_amd64.buildinfo 24c339b0bc4a1798291a87cfb450cc5877e0192215ebc85b511cb39348cba3e0 2277892 phyx_1.3.1+ds-2_amd64.deb Files: ce5379d7793fc5b748037b2d69c7ca5b 74132912 debug optional phyx-dbgsym_1.3.1+ds-2_amd64.deb 2af455fdf8e7847a224da53724e05c43 7313 science optional phyx_1.3.1+ds-2_amd64.buildinfo 43e96adeb9a04b058a37066a591ff403 2277892 science optional phyx_1.3.1+ds-2_amd64.deb Wed May 8 05:10:56 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_37-10337.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ornYqdEU/phyx_1.3.1+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ornYqdEU/phyx_1.3.1+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ornYqdEU/phyx_1.3.1+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ornYqdEU/b1/phyx_1.3.1+ds-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ornYqdEU/b2/phyx_1.3.1+ds-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.145s) 1.145s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.802s) 0.802s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.463s CPU time consumed: 1.453s Wed May 8 05:10:58 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Wed May 8 05:10:58 UTC 2024 I: phyx from trixie built successfully and reproducibly on amd64. Wed May 8 05:11:00 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 8 05:11:00 UTC 2024 I: Submitting 12K b1/phyx_1.3.1+ds-2_amd64.buildinfo.asc Wed May 8 05:11:01 UTC 2024 I: Submitting 12K b2/phyx_1.3.1+ds-2_amd64.buildinfo.asc Wed May 8 05:11:01 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 8 05:11:01 UTC 2024 I: Done submitting .buildinfo files. Wed May 8 05:11:01 UTC 2024 I: Removing signed phyx_1.3.1+ds-2_amd64.buildinfo.asc files: removed './b1/phyx_1.3.1+ds-2_amd64.buildinfo.asc' removed './b2/phyx_1.3.1+ds-2_amd64.buildinfo.asc'