Sun May 21 00:02:27 UTC 2023 I: starting to build phyx/bookworm/armhf on jenkins on '2023-05-21 00:02' Sun May 21 00:02:27 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_34/1821/console.log Sun May 21 00:02:27 UTC 2023 I: Downloading source for bookworm/phyx=1.3+ds-2 --2023-05-21 00:02:27-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/phyx/phyx_1.3%2bds-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2002 (2.0K) [text/prs.lines.tag] Saving to: ‘phyx_1.3+ds-2.dsc’ 0K . 100% 124M=0s 2023-05-21 00:02:27 (124 MB/s) - ‘phyx_1.3+ds-2.dsc’ saved [2002/2002] Sun May 21 00:02:27 UTC 2023 I: phyx_1.3+ds-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phyx Binary: phyx Architecture: any Version: 1.3+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/FePhyFoFum/phyx Standards-Version: 4.6.1 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: febdde970f6f44c676047f52c6b4625f1db104fc 1187728 phyx_1.3+ds.orig.tar.xz 8b7cd92f9014cbed1f9bd9145f66b20a040ad9ab 12872 phyx_1.3+ds-2.debian.tar.xz Checksums-Sha256: f465a87b9ef03f11a41a47580b28079909e6edbf7b2bda3bab3ae8b70d92f184 1187728 phyx_1.3+ds.orig.tar.xz 51fc90025a2ec9e7474e3ea7320b570edf76b7fca113eb45affe9c2a544db7fb 12872 phyx_1.3+ds-2.debian.tar.xz Files: cc931be75d35c74f22872985a62bfd44 1187728 phyx_1.3+ds.orig.tar.xz d8e8b4edbfd5e9b1b2e4293298090c41 12872 phyx_1.3+ds-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNzObURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH/aQ//fLtveN19LG09n3a53T1jo7SyFxnVz64f n+P2ZUyVNMFECebX3BH28YgNFuGbmoQGbpGfv6P+CTEJS03Ia8rwVbOcAwpJ9WJ7 3qt5k9bC2YSUMtXA06IQc+sVEVFOp5xVP60wi/FeDeT6E9M4hybC9uf3nHX2RkhU I5wb0XsBPtbt8huID2IjeBNEMeDoK1KovWaqhqJi918HMYco+O8p7Ng+0SJ5PiDk db1y0Zf2JPBBFrXYPUdcYjKxyeU1CLflqj1B3MK0/xeiDhLymOApX4bM2xzLOu2S PEDDYXZD8l+qP1S8QuQESR3ElKXXSuF7Ycf3kombRITesdKF/PIijH7nVYdjg0Kj +8HU0fyEcUSiQw8LmoRcT7nLK0w9PSqUkyAD2RXmiTVw3bApqDsl6LuLOTDo55o8 arWlqOdfVZ6N6khJtvB7q0qB9CwfN+8jq+BK9KLtNDUkMUs+uF21FcXd0wx9pPV/ gUahPlcGZUgwP7dVG7EmZF9uWEye+qMCTMZR93/xp2ToQsOqlIycH6q8pJ2lKUE3 9docQtoJeCZs7xF0BxnjJCGqtpvvLanX3a8P/dwXNAKE9Y/nCxWa/FW4PfSktqoW ZlxW54QFkbw38LCg0ZT1vXzbWkv4bRF+3fr87EvA0kKinzLKpqy4HY59trtXMXv4 UyHvyAnoRhM= =8YXv -----END PGP SIGNATURE----- Sun May 21 00:02:28 UTC 2023 I: Checking whether the package is not for us Sun May 21 00:02:28 UTC 2023 I: Starting 1st build on remote node virt32c-armhf-rb.debian.net. Sun May 21 00:02:28 UTC 2023 I: Preparing to do remote build '1' on virt32c-armhf-rb.debian.net. Sun May 21 00:15:59 UTC 2023 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 20 12:02:35 -12 2023 I: pbuilder-time-stamp: 1684627355 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [phyx_1.3+ds-2.dsc] I: copying [./phyx_1.3+ds.orig.tar.xz] I: copying [./phyx_1.3+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 14 19:03:17 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phyx_1.3+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting phyx in phyx-1.3+ds dpkg-source: info: unpacking phyx_1.3+ds.orig.tar.xz dpkg-source: info: unpacking phyx_1.3+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying build-more-programs.patch dpkg-source: info: applying i386.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9079/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='a17a52ac57f84887807fc1947f3142c3' 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='9079' 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.BXsB7MPg/pbuilderrc_V6X7 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BXsB7MPg/b1 --logfile b1/build.log phyx_1.3+ds-2.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32c 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/9079/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: armhf 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 ... 19329 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} libarmadillo11{a} libarpack2{a} libarpack2-dev{a} libblas-dev{a} libblas3{a} libbrotli1{a} libcurl4{a} libcurl4-openssl-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsuperlu-dev{a} libsuperlu5{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 82 newly installed, 0 to remove and 0 not upgraded. Need to get 37.7 MB of archives. After unpacking 144 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf hdf5-helpers armhf 1.10.8+repack1-1 [27.9 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libaec0 armhf 1.0.6-1+b1 [19.8 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libsz2 armhf 1.0.6-1+b1 [7864 B] Get: 45 http://deb.debian.org/debian bookworm/main armhf libaec-dev armhf 1.0.6-1+b1 [18.1 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf libarpack2 armhf 3.8.0-3 [82.5 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libsuperlu5 armhf 5.3.0+dfsg1-2+b1 [139 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libarmadillo11 armhf 1:11.4.2+dfsg-1 [96.6 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libblas-dev armhf 3.11.0-2 [115 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf liblapack-dev armhf 3.11.0-2 [1798 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libarpack2-dev armhf 3.8.0-3 [99.7 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libhdf5-103-1 armhf 1.10.8+repack1-1 [1183 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libhdf5-fortran-102 armhf 1.10.8+repack1-1 [82.1 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-100 armhf 1.10.8+repack1-1 [65.3 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-fortran-100 armhf 1.10.8+repack1-1 [38.8 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libhdf5-cpp-103-1 armhf 1.10.8+repack1-1 [119 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-cpp-100 armhf 1.10.8+repack1-1 [25.2 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [260 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libcurl4-openssl-dev armhf 7.88.1-9 [453 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libssl-dev armhf 3.0.8-1 [2132 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libhdf5-dev armhf 1.10.8+repack1-1 [2573 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libsuperlu-dev armhf 5.3.0+dfsg1-2+b1 [22.4 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libarmadillo-dev armhf 1:11.4.2+dfsg-1 [403 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libnlopt0 armhf 2.7.1-4+b4 [141 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libnlopt-dev armhf 2.7.1-4+b4 [46.4 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf libnlopt-cxx0 armhf 2.7.1-4+b4 [159 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libnlopt-cxx-dev armhf 2.7.1-4+b4 [13.2 kB] Fetched 37.7 MB in 2s (18.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.2-6) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_armhf.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:armhf (3.11.2-6) ... Setting up libexpat1:armhf (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19645 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_armhf.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../3-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_armhf.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20079 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_armhf.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../03-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../25-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-12_armhf.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../31-hdf5-helpers_1.10.8+repack1-1_armhf.deb ... Unpacking hdf5-helpers (1.10.8+repack1-1) ... Selecting previously unselected package libaec0:armhf. Preparing to unpack .../32-libaec0_1.0.6-1+b1_armhf.deb ... Unpacking libaec0:armhf (1.0.6-1+b1) ... Selecting previously unselected package libsz2:armhf. Preparing to unpack .../33-libsz2_1.0.6-1+b1_armhf.deb ... Unpacking libsz2:armhf (1.0.6-1+b1) ... Selecting previously unselected package libaec-dev:armhf. Preparing to unpack .../34-libaec-dev_1.0.6-1+b1_armhf.deb ... Unpacking libaec-dev:armhf (1.0.6-1+b1) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../35-libblas3_3.11.0-2_armhf.deb ... Unpacking libblas3:armhf (3.11.0-2) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../36-libgfortran5_12.2.0-14_armhf.deb ... Unpacking libgfortran5:armhf (12.2.0-14) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../37-liblapack3_3.11.0-2_armhf.deb ... Unpacking liblapack3:armhf (3.11.0-2) ... Selecting previously unselected package libarpack2:armhf. Preparing to unpack .../38-libarpack2_3.8.0-3_armhf.deb ... Unpacking libarpack2:armhf (3.8.0-3) ... Selecting previously unselected package libsuperlu5:armhf. Preparing to unpack .../39-libsuperlu5_5.3.0+dfsg1-2+b1_armhf.deb ... Unpacking libsuperlu5:armhf (5.3.0+dfsg1-2+b1) ... Selecting previously unselected package libarmadillo11. Preparing to unpack .../40-libarmadillo11_1%3a11.4.2+dfsg-1_armhf.deb ... Unpacking libarmadillo11 (1:11.4.2+dfsg-1) ... Selecting previously unselected package libblas-dev:armhf. Preparing to unpack .../41-libblas-dev_3.11.0-2_armhf.deb ... Unpacking libblas-dev:armhf (3.11.0-2) ... Selecting previously unselected package liblapack-dev:armhf. Preparing to unpack .../42-liblapack-dev_3.11.0-2_armhf.deb ... Unpacking liblapack-dev:armhf (3.11.0-2) ... Selecting previously unselected package libarpack2-dev:armhf. Preparing to unpack .../43-libarpack2-dev_3.8.0-3_armhf.deb ... Unpacking libarpack2-dev:armhf (3.8.0-3) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../44-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../45-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../46-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../47-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../48-libnghttp2-14_1.52.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../49-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../50-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../51-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:armhf. Preparing to unpack .../52-libcurl4_7.88.1-9_armhf.deb ... Unpacking libcurl4:armhf (7.88.1-9) ... Selecting previously unselected package libhdf5-103-1:armhf. Preparing to unpack .../53-libhdf5-103-1_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-103-1:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-fortran-102:armhf. Preparing to unpack .../54-libhdf5-fortran-102_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-fortran-102:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-100:armhf. Preparing to unpack .../55-libhdf5-hl-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-fortran-100:armhf. Preparing to unpack .../56-libhdf5-hl-fortran-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-fortran-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-cpp-103-1:armhf. Preparing to unpack .../57-libhdf5-cpp-103-1_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-cpp-103-1:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-cpp-100:armhf. Preparing to unpack .../58-libhdf5-hl-cpp-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-cpp-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../59-zlib1g-dev_1%3a1.2.13.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../60-libjpeg62-turbo_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-2) ... Selecting previously unselected package libjpeg62-turbo-dev:armhf. Preparing to unpack .../61-libjpeg62-turbo-dev_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg62-turbo-dev:armhf (1:2.1.5-2) ... Selecting previously unselected package libjpeg-dev:armhf. Preparing to unpack .../62-libjpeg-dev_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg-dev:armhf (1:2.1.5-2) ... Selecting previously unselected package libcurl4-openssl-dev:armhf. Preparing to unpack .../63-libcurl4-openssl-dev_7.88.1-9_armhf.deb ... Unpacking libcurl4-openssl-dev:armhf (7.88.1-9) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../64-libssl-dev_3.0.8-1_armhf.deb ... Unpacking libssl-dev:armhf (3.0.8-1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../65-libhdf5-dev_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-dev (1.10.8+repack1-1) ... Selecting previously unselected package libsuperlu-dev:armhf. Preparing to unpack .../66-libsuperlu-dev_5.3.0+dfsg1-2+b1_armhf.deb ... Unpacking libsuperlu-dev:armhf (5.3.0+dfsg1-2+b1) ... Selecting previously unselected package libarmadillo-dev. Preparing to unpack .../67-libarmadillo-dev_1%3a11.4.2+dfsg-1_armhf.deb ... Unpacking libarmadillo-dev (1:11.4.2+dfsg-1) ... Selecting previously unselected package libnlopt0:armhf. Preparing to unpack .../68-libnlopt0_2.7.1-4+b4_armhf.deb ... Unpacking libnlopt0:armhf (2.7.1-4+b4) ... Selecting previously unselected package libnlopt-dev:armhf. Preparing to unpack .../69-libnlopt-dev_2.7.1-4+b4_armhf.deb ... Unpacking libnlopt-dev:armhf (2.7.1-4+b4) ... Selecting previously unselected package libnlopt-cxx0:armhf. Preparing to unpack .../70-libnlopt-cxx0_2.7.1-4+b4_armhf.deb ... Unpacking libnlopt-cxx0:armhf (2.7.1-4+b4) ... Selecting previously unselected package libnlopt-cxx-dev:armhf. Preparing to unpack .../71-libnlopt-cxx-dev_2.7.1-4+b4_armhf.deb ... Unpacking libnlopt-cxx-dev:armhf (2.7.1-4+b4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libpsl5:armhf (0.21.2-1) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up hdf5-helpers (1.10.8+repack1-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libnlopt0:armhf (2.7.1-4+b4) ... Setting up file (1:5.44-3) ... Setting up libaec0:armhf (1.0.6-1+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... 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Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/phyx-1.3+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+ds-2_source.changes dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 1.3+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phyx-1.3+ds' rm -rf src/phyx.logfile if [ -r src/Makefile ]; then \ /usr/bin/make -C src distclean; \ fi make[1]: Leaving directory '/build/phyx-1.3+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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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 -j3 make[1]: Entering directory '/build/phyx-1.3+ds/src' g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" utils.cpp: In function ‘void v_mean_variance(std::vector&, double&, double&)’: utils.cpp:456:21: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 456 | std::bind2nd(std::minus(), mn)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_function.h:1438, from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from utils.cpp:1: /usr/include/c++/12/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:467:21: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 467 | std::bind2nd(std::minus(), meann)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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:542:69: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = multiplies; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 542 | std::transform(res.begin(), res.end(), res.begin(), std::bind1st(std::multiplies(), 0.5)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from utils.cpp:6: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/vector:70, from pairwise_alignment.cpp:1: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘double nw(Sequence&, Sequence&, std::map >&, double, std::string&, std::string&)’ at pairwise_alignment.cpp:28:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘double sw(Sequence&, Sequence&, std::map >&, double, std::string&, std::string&)’ at pairwise_alignment.cpp:118:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/vector:70, from tree_utils.cpp:3: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘bool postorder_ultrametricity_check(Node*, bool&)’ at tree_utils.cpp:547:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘void set_node_heights(Node*)’ at tree_utils.cpp:510:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from bd_sim.cpp:3: /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void BirthDeathSimulator::node_death(Node*)’ at bd_sim.cpp:186:22: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void BirthDeathSimulator::node_death(Node*)’ at bd_sim.cpp:187:34: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void BirthDeathSimulator::node_death(Node*)’ at bd_sim.cpp:187:55: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void BirthDeathSimulator::node_birth(Node*)’ at bd_sim.cpp:198:20: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void BirthDeathSimulator::node_birth(Node*)’ at bd_sim.cpp:199:21: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘Tree* BirthDeathSimulator::make_tree(const bool&)’ at bd_sim.cpp:59:21: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘Tree* BirthDeathSimulator::make_tree(const bool&)’ at bd_sim.cpp:84:33: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘Tree* BirthDeathSimulator::make_tree(const bool&)’ at bd_sim.cpp:95:40: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/vector:70, from main_bp.cpp:4: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/vector:70, from log_manip.cpp:2: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void LogManipulator::store_sample(const std::string&)’ at log_manip.cpp:287:35: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from seq_info.cpp:2: /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void SeqInfo::count_chars_indiv_seq(std::string&)’ at seq_info.cpp:39:24: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void SeqInfo::count_chars_indiv_seq(std::string&)’ at seq_info.cpp:44:28: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void SeqInfo::count_chars_indiv_seq(std::string&)’ at seq_info.cpp:46:21: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void SeqInfo::print_summary_table_whole_alignment()’ at seq_info.cpp:270:71: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void SeqInfo::print_summary_table_whole_alignment()’ at seq_info.cpp:271:56: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" 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++/12/bits/stl_function.h:1438, from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from nj.cpp:1: /usr/include/c++/12/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/vector:70, from state_reconstructor.cpp:2: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BranchSegment&}; _Tp = BranchSegment; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from rate_model.cpp:1: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const arma::Mat&}; _Tp = arma::Mat; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = arma::Mat; _Alloc = std::allocator >]’, inlined from ‘void RateModel::set_n_qs(int)’ at rate_model.cpp:110:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BranchSegment; _Alloc = std::allocator]’, inlined from ‘void StateReconstructor::set_tree(Tree*)’ at state_reconstructor.cpp:85:76: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BranchSegment; _Alloc = std::allocator]’, inlined from ‘void StateReconstructor::set_tree(Tree*)’ at state_reconstructor.cpp:95:64: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from state_reconstructor.cpp:3: /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = double; _Tp = arma::Mat >; _Compare = std::less; _Alloc = std::allocator > > >]’, inlined from ‘VectorNodeObject StateReconstructor::conditionals_periods(Node&)’ at state_reconstructor.cpp:253:66: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = double; _Tp = arma::Mat >; _Compare = std::less; _Alloc = std::allocator > > >]’, inlined from ‘VectorNodeObject StateReconstructor::conditionals(Node&)’ at state_reconstructor.cpp:217:46: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = double; _Tp = arma::Mat >; _Compare = std::less; _Alloc = std::allocator > > >]’, inlined from ‘void StateReconstructor::reverse(Node*)’ at state_reconstructor.cpp:398:57: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator*, vector > >; _ForwardIterator = arma::Mat*]’: /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _ForwardIterator = arma::Mat*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator*, vector > >; _ForwardIterator = arma::Mat*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator*, vector > >; _ForwardIterator = arma::Mat*; _Tp = arma::Mat]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = arma::Mat; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from ‘RateModel::RateModel(const RateModel&)’ at rate_model.h:11:7: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _ForwardIterator = arma::Mat*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator*, vector > >; _ForwardIterator = arma::Mat*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator*, vector > >; _ForwardIterator = arma::Mat*; _Tp = arma::Mat]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = arma::Mat; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = arma::Mat; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from ‘RateModel& RateModel::operator=(const RateModel&)’ at rate_model.h:11:7: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/vector:70, from main_seqgen.cpp:4: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void parse_comma_list(std::string&, std::vector<_RealType>&) [with T = double]’ at utils.h:48:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/map:60, from /usr/include/armadillo:44, from cont_models.cpp:4: /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double calc_bm_prune(Tree*, double)’ at cont_models.cpp:241:30: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double calc_bm_prune(Tree*, double)’ at cont_models.cpp:245:56: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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" In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from bd_fit.cpp:6: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘void BDFit::fit_bd()’ at bd_fit.cpp:102:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘void BDFit::fit_bd()’ at bd_fit.cpp:102:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -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++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxaa2cdn" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now In file included from /usr/include/c++/12/vector:70, from optimize_cont_models_nlopt.cpp:2: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_nlopt(arma::rowvec&, arma::mat&, bool)’ at optimize_cont_models_nlopt.cpp:128:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_nlopt(arma::rowvec&, arma::mat&, bool)’ at optimize_cont_models_nlopt.cpp:129:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_nlopt(arma::rowvec&, arma::mat&, bool)’ at optimize_cont_models_nlopt.cpp:130:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ cat man/pxaa2cdn.1.in > man/pxaa2cdn.1 building pxbdsim g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxbdsim" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxbdsim.1.in > man/pxbdsim.1 building pxboot g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxboot" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_ou_nlopt(arma::rowvec&, arma::mat&)’ at optimize_cont_models_nlopt.cpp:157:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_ou_nlopt(arma::rowvec&, arma::mat&)’ at optimize_cont_models_nlopt.cpp:158:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_ou_nlopt(arma::rowvec&, arma::mat&)’ at optimize_cont_models_nlopt.cpp:159:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_ou_nlopt(arma::rowvec&, arma::mat&)’ at optimize_cont_models_nlopt.cpp:160:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ cat man/pxboot.1.in > man/pxboot.1 building pxbp g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxbp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_bp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_bl(Tree*)’ at optimize_cont_models_nlopt.cpp:192:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector optimize_single_rate_bm_bl(Tree*)’ at optimize_cont_models_nlopt.cpp:193:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ cat man/pxbp.1.in > man/pxbp.1 building pxcat g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxcat.1.in > man/pxcat.1 building pxclsq g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxclsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxclsq.1.in > man/pxclsq.1 building pxcltr g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcltr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now building pxcolt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcolt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxcltr.1.in > man/pxcltr.1 building pxcomp g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now In file included from /usr/include/c++/12/vector:70, from main_strec.cpp:4: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cat man/pxcolt.1.in > man/pxcolt.1 In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void parse_comma_list(std::string&, std::vector&) [with T = double]’ at utils.h:48:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ building pxconsq g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxconsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxcomp.1.in > man/pxcomp.1 building pxfqfilt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxfqfilt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxconsq.1.in > man/pxconsq.1 building pxlog g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlog" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxfqfilt.1.in > man/pxfqfilt.1 bulding pxlssq g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlssq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxlog.1.in > man/pxlog.1 building pxlstr g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlstr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxlssq.1.in > man/pxlssq.1 building pxmono g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmono" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mono.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxlstr.1.in > man/pxlstr.1 building pxmrca g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrca" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxmono.1.in > man/pxmono.1 building pxmrcacut g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrcacut" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca_cut.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RateModel&}; _Tp = RateModel; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RateModel; _Alloc = std::allocator]’: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ cat man/pxmrca.1.in > man/pxmrca.1 building pxmrcaname g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrcaname" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca_name.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxmrcacut.1.in > man/pxmrcacut.1 building pxnw g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxnw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxmrcaname.1.in > man/pxmrcaname.1 building pxpoly g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxpoly" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxnw.1.in > man/pxnw.1 building pxrecode g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrecode" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxpoly.1.in > man/pxpoly.1 building pxrevcomp g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrevcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxrecode.1.in > man/pxrecode.1 building pxrls g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrls" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxrevcomp.1.in > man/pxrevcomp.1 building pxupgma g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxupgma" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxrls.1.in > man/pxrls.1 building pxrlt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrlt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxupgma.1.in > man/pxupgma.1 building pxnj g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxnj" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxrlt.1.in > man/pxrlt.1 building pxrmk g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrmk" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rmk.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxnj.1.in > man/pxnj.1 building pxrms g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrms" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxrmk.1.in > man/pxrmk.1 building pxrmt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrmt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rmt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxrms.1.in > man/pxrms.1 building pxrr g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxrmt.1.in > man/pxrmt.1 building pxs2fa g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxrr.1.in > man/pxrr.1 building pxs2nex g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxs2fa.1.in > man/pxs2fa.1 building pxs2phy g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2phy" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxs2nex.1.in > man/pxs2nex.1 building pxseqgen g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxseqgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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/pxs2phy.1.in > man/pxs2phy.1 building pxssort g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxssort" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxseqgen.1.in > man/pxseqgen.1 building pxsstat g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxsstat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxssort.1.in > man/pxssort.1 building pxsw g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxsw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxsstat.1.in > man/pxsstat.1 building pxt2new g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxt2new" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_t2new.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxsw.1.in > man/pxsw.1 building pxt2nex g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxt2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_t2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxt2new.1.in > man/pxt2new.1 building pxtcol g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtcol" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_tcol.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxt2nex.1.in > man/pxt2nex.1 building pxtcomb g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtcomb" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_tcomb.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxtcol.1.in > man/pxtcol.1 building pxtgen g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxtcomb.1.in > man/pxtcomb.1 building pxtlate g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtlate" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxtgen.1.in > man/pxtgen.1 building pxtrt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtrt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_trt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxtlate.1.in > man/pxtlate.1 building pxtscale g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtscale" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxtrt.1.in > man/pxtrt.1 building pxvcf2fa g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxvcf2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 -Wl,-z,relro -Wl,-z,now cat man/pxtscale.1.in > man/pxtscale.1 building pxbdfit g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxbdfit" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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 building pxcontrates g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxcontrates" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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/pxvcf2fa.1.in > man/pxvcf2fa.1 building pxstrec g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxstrec" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math 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/pxbdfit.1.in > man/pxbdfit.1 cat man/pxcontrates.1.in > man/pxcontrates.1 cat man/pxstrec.1.in > man/pxstrec.1 make[1]: Leaving directory '/build/phyx-1.3+ds/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/phyx-1.3+ds' cd src && python3 run_tests.py character: 0 character: 1 character: 2 ================= TESTING pxaa2cdn 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 sites 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 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 PASSED ================= TESTING pxrlt 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 (93 tests) FAILED PROGRAMS: 0 (0 tests) PROGRAMS WITHOUT TESTS: 2 make[1]: Leaving directory '/build/phyx-1.3+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/phyx-1.3+ds' mkdir -p /build/phyx-1.3+ds/debian/phyx/usr/bin dh_auto_install -- PREFIX=/build/phyx-1.3+ds/debian/phyx/usr cd src && make -j3 install DESTDIR=/build/phyx-1.3\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/build/phyx-1.3\+ds/debian/phyx/usr make[2]: Entering directory '/build/phyx-1.3+ds/src' mkdir -p /build/phyx-1.3+ds/debian/phyx/usr/bin && install -m 0755 px* /build/phyx-1.3+ds/debian/phyx/usr/bin mkdir -p /build/phyx-1.3+ds/debian/phyx/usr/share/man/man1 && install -m 0755 man/px*.1 /build/phyx-1.3+ds/debian/phyx/usr/share/man/man1 make[2]: Leaving directory '/build/phyx-1.3+ds/src' #echo "#!/usr/bin/python3" > /build/phyx-1.3+ds/debian/phyx/usr/bin/Phyx_Gui #cat src/Phyx_Gui.py >> /build/phyx-1.3+ds/debian/phyx/usr/bin/Phyx_Gui make[1]: Leaving directory '/build/phyx-1.3+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_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory '/build/phyx-1.3+ds' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/phyx-1.3+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 dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxsw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrls contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxlog contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcolt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrmk contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxnw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtrt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxpoly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxfqfilt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrms contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcltr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtlate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxboot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxstrec contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxs2phy contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxaa2cdn contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxnj contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrevcomp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxt2new contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxvcf2fa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxs2fa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxupgma contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtcomb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtcol contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxbdsim contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxsstat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcomp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxt2nex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxlssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrlt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxmrca contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxssort contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxmono contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrecode contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxs2nex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxlstr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcontrates contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxconsq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxmrcaname contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxbdfit contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxclsq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxbp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxmrcacut contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtgen contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxseqgen contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtscale contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrmt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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+ds-2_armhf.deb'. dpkg-deb: building package 'phyx' in '../phyx_1.3+ds-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../phyx_1.3+ds-2_armhf.buildinfo dpkg-genchanges --build=binary -O../phyx_1.3+ds-2_armhf.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/9079 and its subdirectories I: Current time: Sat May 20 12:13:34 -12 2023 I: pbuilder-time-stamp: 1684628014 Sun May 21 00:16:01 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Sun May 21 00:16:01 UTC 2023 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Sun May 21 00:42:06 UTC 2023 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Sun May 21 00:42:09 UTC 2023 I: phyx_1.3+ds-2_armhf.changes: Format: 1.8 Date: Tue, 15 Nov 2022 07:43:33 +0100 Source: phyx Binary: phyx phyx-dbgsym Architecture: armhf Version: 1.3+ds-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: phyx - UNIX-style phylogenetic analyses on trees and sequences Changes: phyx (1.3+ds-2) unstable; urgency=medium . [ Olek Wojnar ] * Remove unneeded dependency on libatlas-cpp . [ Andreas Tille ] * Standards-Version: 4.6.1 (routine-update) * No tab in license text (routine-update) Checksums-Sha1: c9eb36cbc3e1ce8ff256087c128f3b56a1b2627d 66876672 phyx-dbgsym_1.3+ds-2_armhf.deb 066c975e9193e2a919f7402991d43f7d3ec5554f 6850 phyx_1.3+ds-2_armhf.buildinfo 1e10844dfffa788b6f3671f7e26e045ee4a234fa 1724948 phyx_1.3+ds-2_armhf.deb Checksums-Sha256: 4e0201fe46e1a0eb06e780bb58f9cbfacd5923eb81f9dfbbc7a8acf7bd209d4b 66876672 phyx-dbgsym_1.3+ds-2_armhf.deb 9038c2f4dce421431bbd11b317c76ed7f72226e1ac6227efd8d6619f7b2dfc76 6850 phyx_1.3+ds-2_armhf.buildinfo d8593d24e91f8dbdeabc8f4e2feb0e6db2cf3feb3578593c0b4a558d64c47158 1724948 phyx_1.3+ds-2_armhf.deb Files: a9f63222b90f40278fca4e659e88e17c 66876672 debug optional phyx-dbgsym_1.3+ds-2_armhf.deb a79ee57271777bd088f3cd4e06e7de0b 6850 science optional phyx_1.3+ds-2_armhf.buildinfo e3761f8bc5de7ff6a2dcae8668e5f71b 1724948 science optional phyx_1.3+ds-2_armhf.deb Sun May 21 00:42:10 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.BXsB7MPg/phyx_1.3+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.BXsB7MPg/phyx_1.3+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.BXsB7MPg/phyx_1.3+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.BXsB7MPg/b1/phyx_1.3+ds-2_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.BXsB7MPg/b2/phyx_1.3+ds-2_armhf.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: 1.095s) 1.095s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.765s) 0.765s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sun May 21 00:42:14 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Sun May 21 00:42:14 UTC 2023 I: phyx from bookworm built successfully and reproducibly on armhf. Sun May 21 00:42:15 UTC 2023 I: Submitting .buildinfo files to external archives: Sun May 21 00:42:15 UTC 2023 I: Submitting 8.0K b1/phyx_1.3+ds-2_armhf.buildinfo.asc Sun May 21 00:42:16 UTC 2023 I: Submitting 8.0K b2/phyx_1.3+ds-2_armhf.buildinfo.asc Sun May 21 00:42:17 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 21 00:42:17 UTC 2023 I: Done submitting .buildinfo files. Sun May 21 00:42:17 UTC 2023 I: Removing signed phyx_1.3+ds-2_armhf.buildinfo.asc files: removed './b1/phyx_1.3+ds-2_armhf.buildinfo.asc' removed './b2/phyx_1.3+ds-2_armhf.buildinfo.asc'