Wed Nov 13 05:37:00 UTC 2024 I: starting to build phyx/trixie/armhf on jenkins on '2024-11-13 05:36' Wed Nov 13 05:37:00 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_12/9767/console.log Wed Nov 13 05:37:00 UTC 2024 I: Downloading source for trixie/phyx=1.3.2+ds-1 --2024-11-13 05:37:01-- http://deb.debian.org/debian/pool/main/p/phyx/phyx_1.3.2%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2177 (2.1K) [text/prs.lines.tag] Saving to: ‘phyx_1.3.2+ds-1.dsc’ 0K .. 100% 230M=0s 2024-11-13 05:37:01 (230 MB/s) - ‘phyx_1.3.2+ds-1.dsc’ saved [2177/2177] Wed Nov 13 05:37:01 UTC 2024 I: phyx_1.3.2+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phyx Binary: phyx Architecture: any Version: 1.3.2+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/FePhyFoFum/phyx Standards-Version: 4.7.0 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:any, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libarmadillo-dev Package-List: phyx deb science optional arch=any Checksums-Sha1: ff5e6371d8f9fdc2366e08b54ef844468fd23308 1213536 phyx_1.3.2+ds.orig.tar.xz 1338a7738445072cf15b6de8567be8566fdf46ab 10420 phyx_1.3.2+ds-1.debian.tar.xz Checksums-Sha256: 10cb2d18254f0779fbd8fb6c9dfd9b710054e1800b2453c3403722107c2ab392 1213536 phyx_1.3.2+ds.orig.tar.xz 019134a6fe66f4e6c99d76e93836f4ec51156211e36565f271f06ddd19454bb2 10420 phyx_1.3.2+ds-1.debian.tar.xz Files: 84966df55591acec4d10fe82cc8ac7b8 1213536 phyx_1.3.2+ds.orig.tar.xz 143b92b74fecd9d02a4db48a8defee8a 10420 phyx_1.3.2+ds-1.debian.tar.xz Dgit: c8f8e06091122a0c36e72e9f48e3a433d2529446 debian archive/debian/1.3.2+ds-1 https://git.dgit.debian.org/phyx -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcmSs8UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrcjg/+NJ9fE0CY3YK5U/bixp6Iy/a/ewjN vkYRGSm6oJiglMWqf5szTYmhnPcWIdtxuSLSBlNZFf7DtvqotnLoAOnNweLK/N+B LWeWhLBYCRcQNENHNCDMBMSi3ITZDDW1ZJGxLBFNXsq7AgY6OybnfRowwmyAQXTN HOz+KPwTJby3T17x3013roU9Plm/XOhjYTIG98/ayr/EdA1RJL7TTmcUxAsc77ve ycbO79GHYg/AmDBG42XbqD5qPX/4wBLzrJ/wlMVa3EIe2tZoLdBOEL4+7yuy996P 2QkmDbWUhsXnz+70oQyXv1h+uT33kopG2aBsm5NJkgCnK5xt50tQGJgAqAsXj434 Qny2dN6rMJx8uYHs5Dp4MByXOCLopOFUldj1J2xAYi28ECaIjWeYvjlCYpQQ27wb 7ZcUnN4ZBe926kA9oyY3rtMtl+svjKguEsDwAhU0HSCErP8y2ah7JJJLysqd2Hmi 5X1RR9TW/qMBF2wrYRkYOBdGG54MdNOemCAn+gY5c0Zbnj3yWy6VyGnRLcLLjkRi P5yXqq6by/pudHzrU1tFrNfCpWVAEEZkK7u58iA1DQSUB6vfMdFJHMHwBeyG4lCh 0SxFSB0bokUbC8RxMQ4Qctof7cxNlkY6zmYajQtPfLCIniCW3aCkJUIP8GEPAbSZ H1LNLGDSLm820O0= =2Swv -----END PGP SIGNATURE----- Wed Nov 13 05:37:01 UTC 2024 I: Checking whether the package is not for us Wed Nov 13 05:37:01 UTC 2024 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Wed Nov 13 05:37:01 UTC 2024 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Wed Nov 13 05:52:20 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Nov 12 17:37:09 -12 2024 I: pbuilder-time-stamp: 1731476229 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [phyx_1.3.2+ds-1.dsc] I: copying [./phyx_1.3.2+ds.orig.tar.xz] I: copying [./phyx_1.3.2+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 2 15:52:47 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phyx_1.3.2+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting phyx in phyx-1.3.2+ds dpkg-source: info: unpacking phyx_1.3.2+ds.orig.tar.xz dpkg-source: info: unpacking phyx_1.3.2+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying build-more-programs.patch dpkg-source: info: applying whatis.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11703/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='a14f9049bef344bb85653e3a541ff9c4' 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='11703' 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.QANk4eo2/pbuilderrc_TRo4 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QANk4eo2/b1 --logfile b1/build.log phyx_1.3.2+ds-1.dsc' SUDO_GID='114' SUDO_UID='108' 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 virt64a 6.1.0-27-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/11703/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:any, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libarmadillo-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19690 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3:any. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-cxx-dev; however: Package libnlopt-cxx-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-dev; however: Package libnlopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libarmadillo-dev; however: Package libarmadillo-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{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} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarmadillo-dev{a} libarmadillo14{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldap-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libnsl2{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsuperlu-dev{a} libsuperlu6{a} libsuperlu7{a} libsz2{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 48.3 MB of archives. After unpacking 172 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.7-3 [800 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.3-2 [83.1 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.7-3 [1808 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 12 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1819 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-9 [88.8 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf comerr-dev armhf 2.1-1.47.1-1+b1 [54.3 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.1 [604 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf hdf5-helpers armhf 1.10.10+repack-4 [23.5 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libgssrpc4t64 armhf 1.21.3-3 [52.5 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libkadm5clnt-mit12 armhf 1.21.3-3 [37.0 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libkdb5-10t64 armhf 1.21.3-3 [37.1 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libkadm5srv-mit12 armhf 1.21.3-3 [46.7 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf krb5-multidev armhf 1.21.3-3 [126 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libaec0 armhf 1.1.3-1+b1 [21.9 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libsz2 armhf 1.1.3-1+b1 [8036 B] Get: 61 http://deb.debian.org/debian trixie/main armhf libaec-dev armhf 1.1.3-1+b1 [19.3 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-3+b1 [111 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14.2.0-8 [263 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-3+b1 [1828 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libarpack2t64 armhf 3.9.1-1.1+b1 [85.0 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libsuperlu6 armhf 6.0.1+dfsg1-1+b1 [139 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libarmadillo14 armhf 1:14.0.1+dfsg-2 [99.8 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libblas-dev armhf 3.12.0-3+b1 [121 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf liblapack-dev armhf 3.12.0-3+b1 [1930 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libarpack2-dev armhf 3.9.1-1.1+b1 [103 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b5 [296 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libcurl4t64 armhf 8.11.0-1 [303 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libhdf5-103-1t64 armhf 1.10.10+repack-4 [1196 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libhdf5-fortran-102t64 armhf 1.10.10+repack-4 [78.5 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4 [62.3 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libhdf5-hl-fortran-100t64 armhf 1.10.10+repack-4 [35.1 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libhdf5-cpp-103-1t64 armhf 1.10.10+repack-4 [121 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libhdf5-hl-cpp-100t64 armhf 1.10.10+repack-4 [21.0 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-3+b1 [263 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libjpeg-dev armhf 1:2.1.5-3+b1 [72.2 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libbrotli-dev armhf 1.1.0-2+b5 [294 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libkrb5-dev armhf 1.21.3-3 [15.8 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libldap-dev armhf 2.5.18+dfsg-3+b1 [282 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b2 [328 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b2 [593 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libunbound8 armhf 1.22.0-1 [539 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libgnutls-dane0t64 armhf 3.8.6-2+b1 [432 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libgnutls-openssl27t64 armhf 3.8.6-2+b1 [432 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libp11-kit-dev armhf 0.25.5-2+b1 [208 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libgnutls28-dev armhf 3.8.6-2+b1 [1322 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libssl-dev armhf 3.3.2-2 [2385 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libzstd-dev armhf 1.5.6+dfsg-1+b1 [327 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf libcurl4-openssl-dev armhf 8.11.0-1 [423 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libhdf5-dev armhf 1.10.10+repack-4 [2616 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libsuperlu7 armhf 7.0.0+dfsg1-2 [142 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf libsuperlu-dev armhf 7.0.0+dfsg1-2 [21.9 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf libarmadillo-dev armhf 1:14.0.1+dfsg-2 [413 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf libnlopt0 armhf 2.7.1-6 [143 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libnlopt-dev armhf 2.7.1-6 [46.6 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libnlopt-cxx0 armhf 2.7.1-6 [162 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libnlopt-cxx-dev armhf 2.7.1-6 [13.2 kB] Fetched 48.3 MB in 1s (41.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 19690 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.7-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.3-2_armhf.deb ... Unpacking libexpat1:armhf (2.6.3-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_armhf.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:armhf (3.12.7-3) ... Setting up libexpat1:armhf (2.6.3-2) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20010 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_armhf.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../04-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../06-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../07-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../08-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:armhf. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../14-libreadline8t64_8.2-5_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_armhf.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21072 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_armhf.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-9_armhf.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package comerr-dev:armhf. Preparing to unpack .../16-comerr-dev_2.1-1.47.1-1+b1_armhf.deb ... Unpacking comerr-dev:armhf (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../23-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../25-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-0.1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... 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_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../31-hdf5-helpers_1.10.10+repack-4_armhf.deb ... Unpacking hdf5-helpers (1.10.10+repack-4) ... Selecting previously unselected package libgssrpc4t64:armhf. Preparing to unpack .../32-libgssrpc4t64_1.21.3-3_armhf.deb ... Unpacking libgssrpc4t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:armhf. Preparing to unpack .../33-libkadm5clnt-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5clnt-mit12:armhf (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:armhf. Preparing to unpack .../34-libkdb5-10t64_1.21.3-3_armhf.deb ... Unpacking libkdb5-10t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:armhf. Preparing to unpack .../35-libkadm5srv-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5srv-mit12:armhf (1.21.3-3) ... Selecting previously unselected package krb5-multidev:armhf. Preparing to unpack .../36-krb5-multidev_1.21.3-3_armhf.deb ... Unpacking krb5-multidev:armhf (1.21.3-3) ... Selecting previously unselected package libaec0:armhf. Preparing to unpack .../37-libaec0_1.1.3-1+b1_armhf.deb ... Unpacking libaec0:armhf (1.1.3-1+b1) ... Selecting previously unselected package libsz2:armhf. Preparing to unpack .../38-libsz2_1.1.3-1+b1_armhf.deb ... Unpacking libsz2:armhf (1.1.3-1+b1) ... Selecting previously unselected package libaec-dev:armhf. Preparing to unpack .../39-libaec-dev_1.1.3-1+b1_armhf.deb ... Unpacking libaec-dev:armhf (1.1.3-1+b1) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../40-libblas3_3.12.0-3+b1_armhf.deb ... Unpacking libblas3:armhf (3.12.0-3+b1) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../41-libgfortran5_14.2.0-8_armhf.deb ... Unpacking libgfortran5:armhf (14.2.0-8) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../42-liblapack3_3.12.0-3+b1_armhf.deb ... Unpacking liblapack3:armhf (3.12.0-3+b1) ... Selecting previously unselected package libarpack2t64:armhf. Preparing to unpack .../43-libarpack2t64_3.9.1-1.1+b1_armhf.deb ... Unpacking libarpack2t64:armhf (3.9.1-1.1+b1) ... Selecting previously unselected package libsuperlu6:armhf. Preparing to unpack .../44-libsuperlu6_6.0.1+dfsg1-1+b1_armhf.deb ... Unpacking libsuperlu6:armhf (6.0.1+dfsg1-1+b1) ... Selecting previously unselected package libarmadillo14. Preparing to unpack .../45-libarmadillo14_1%3a14.0.1+dfsg-2_armhf.deb ... Unpacking libarmadillo14 (1:14.0.1+dfsg-2) ... Selecting previously unselected package libblas-dev:armhf. Preparing to unpack .../46-libblas-dev_3.12.0-3+b1_armhf.deb ... Unpacking libblas-dev:armhf (3.12.0-3+b1) ... Selecting previously unselected package liblapack-dev:armhf. Preparing to unpack .../47-liblapack-dev_3.12.0-3+b1_armhf.deb ... Unpacking liblapack-dev:armhf (3.12.0-3+b1) ... Selecting previously unselected package libarpack2-dev:armhf. Preparing to unpack .../48-libarpack2-dev_3.9.1-1.1+b1_armhf.deb ... Unpacking libarpack2-dev:armhf (3.9.1-1.1+b1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../49-libbrotli1_1.1.0-2+b5_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b5) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../50-libsasl2-modules-db_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../51-libsasl2-2_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../52-libldap-2.5-0_2.5.18+dfsg-3+b1_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../53-libnghttp2-14_1.64.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.64.0-1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../54-libpsl5t64_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../55-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../56-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl4t64:armhf. Preparing to unpack .../57-libcurl4t64_8.11.0-1_armhf.deb ... Unpacking libcurl4t64:armhf (8.11.0-1) ... Selecting previously unselected package libhdf5-103-1t64:armhf. Preparing to unpack .../58-libhdf5-103-1t64_1.10.10+repack-4_armhf.deb ... Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4) ... Selecting previously unselected package libhdf5-fortran-102t64:armhf. 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Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../64-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../65-libjpeg62-turbo_1%3a2.1.5-3+b1_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Selecting previously unselected package libjpeg62-turbo-dev:armhf. Preparing to unpack .../66-libjpeg62-turbo-dev_1%3a2.1.5-3+b1_armhf.deb ... Unpacking libjpeg62-turbo-dev:armhf (1:2.1.5-3+b1) ... Selecting previously unselected package libjpeg-dev:armhf. Preparing to unpack .../67-libjpeg-dev_1%3a2.1.5-3+b1_armhf.deb ... Unpacking libjpeg-dev:armhf (1:2.1.5-3+b1) ... Selecting previously unselected package libbrotli-dev:armhf. Preparing to unpack .../68-libbrotli-dev_1.1.0-2+b5_armhf.deb ... Unpacking libbrotli-dev:armhf (1.1.0-2+b5) ... Selecting previously unselected package libidn2-dev:armhf. 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Unpacking libunbound8:armhf (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:armhf. Preparing to unpack .../81-libgnutls-dane0t64_3.8.6-2+b1_armhf.deb ... Unpacking libgnutls-dane0t64:armhf (3.8.6-2+b1) ... Selecting previously unselected package libgnutls-openssl27t64:armhf. Preparing to unpack .../82-libgnutls-openssl27t64_3.8.6-2+b1_armhf.deb ... Unpacking libgnutls-openssl27t64:armhf (3.8.6-2+b1) ... Selecting previously unselected package libp11-kit-dev:armhf. Preparing to unpack .../83-libp11-kit-dev_0.25.5-2+b1_armhf.deb ... Unpacking libp11-kit-dev:armhf (0.25.5-2+b1) ... Selecting previously unselected package libtasn1-6-dev:armhf. Preparing to unpack .../84-libtasn1-6-dev_4.19.0-3+b3_armhf.deb ... Unpacking libtasn1-6-dev:armhf (4.19.0-3+b3) ... Selecting previously unselected package nettle-dev:armhf. Preparing to unpack .../85-nettle-dev_3.10-1+b1_armhf.deb ... Unpacking nettle-dev:armhf (3.10-1+b1) ... 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Preparing to unpack .../91-libcurl4-openssl-dev_8.11.0-1_armhf.deb ... Unpacking libcurl4-openssl-dev:armhf (8.11.0-1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../92-libhdf5-dev_1.10.10+repack-4_armhf.deb ... Unpacking libhdf5-dev (1.10.10+repack-4) ... Selecting previously unselected package libsuperlu7:armhf. Preparing to unpack .../93-libsuperlu7_7.0.0+dfsg1-2_armhf.deb ... Unpacking libsuperlu7:armhf (7.0.0+dfsg1-2) ... Selecting previously unselected package libsuperlu-dev:armhf. Preparing to unpack .../94-libsuperlu-dev_7.0.0+dfsg1-2_armhf.deb ... Unpacking libsuperlu-dev:armhf (7.0.0+dfsg1-2) ... Selecting previously unselected package libarmadillo-dev. Preparing to unpack .../95-libarmadillo-dev_1%3a14.0.1+dfsg-2_armhf.deb ... Unpacking libarmadillo-dev (1:14.0.1+dfsg-2) ... Selecting previously unselected package libnlopt0:armhf. Preparing to unpack .../96-libnlopt0_2.7.1-6_armhf.deb ... Unpacking libnlopt0:armhf (2.7.1-6) ... Selecting previously unselected package libnlopt-dev:armhf. Preparing to unpack .../97-libnlopt-dev_2.7.1-6_armhf.deb ... Unpacking libnlopt-dev:armhf (2.7.1-6) ... Selecting previously unselected package libnlopt-cxx0:armhf. Preparing to unpack .../98-libnlopt-cxx0_2.7.1-6_armhf.deb ... Unpacking libnlopt-cxx0:armhf (2.7.1-6) ... Selecting previously unselected package libnlopt-cxx-dev:armhf. Preparing to unpack .../99-libnlopt-cxx-dev_2.7.1-6_armhf.deb ... Unpacking libnlopt-cxx-dev:armhf (2.7.1-6) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libgnutls-openssl27t64:armhf (3.8.6-2+b1) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up libzstd-dev:armhf (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-9) ... Setting up hdf5-helpers (1.10.10+repack-4) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b5) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Setting up libnlopt0:armhf (2.7.1-6) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:armhf (1.1.3-1+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Nov 13 05:38:10 UTC 2024. Universal Time is now: Wed Nov 13 05:38:10 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.0-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libunbound8:armhf (1.22.0-1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Setting up libgnutls-dane0t64:armhf (3.8.6-2+b1) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-3+b1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up comerr-dev:armhf (2.1-1.47.1-1+b1) ... Setting up libssl-dev:armhf (3.3.2-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libidn2-dev:armhf (2.3.7-2+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up libgfortran5:armhf (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libnlopt-cxx0:armhf (2.7.1-6) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libnlopt-dev:armhf (2.7.1-6) ... Setting up libtasn1-6-dev:armhf (4.19.0-3+b3) ... Setting up readline-common (8.2-5) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libbrotli-dev:armhf (1.1.0-2+b5) ... Setting up libp11-kit-dev:armhf (0.25.5-2+b1) ... Setting up libblas-dev:armhf (3.12.0-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up libsz2:armhf (1.1.3-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:armhf (3.12.0-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.22.5-2) ... Setting up libarpack2t64:armhf (3.9.1-1.1+b1) ... Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:armhf (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up libaec-dev:armhf (1.1.3-1+b1) ... Setting up libjpeg-dev:armhf (1:2.1.5-3+b1) ... Setting up libsuperlu6:armhf (6.0.1+dfsg1-1+b1) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Setting up libsuperlu7:armhf (7.0.0+dfsg1-2) ... Setting up pkgconf:armhf (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libnlopt-cxx-dev:armhf (2.7.1-6) ... Setting up libldap-dev:armhf (2.5.18+dfsg-3+b1) ... Setting up liblapack-dev:armhf (3.12.0-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libssh2-1-dev:armhf (1.11.1-1) ... Setting up libreadline8t64:armhf (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libarmadillo14 (1:14.0.1+dfsg-2) ... Setting up libsuperlu-dev:armhf (7.0.0+dfsg1-2) ... Setting up libgnutls28-dev:armhf (3.8.6-2+b1) ... Setting up libnghttp2-dev:armhf (1.64.0-1) ... Setting up libarpack2-dev:armhf (3.9.1-1.1+b1) ... Setting up libcurl4t64:armhf (8.11.0-1) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:armhf (1.21.3-3) ... Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libnsl2:armhf (1.3.0-3+b3) ... Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4) ... Setting up libkadm5clnt-mit12:armhf (1.21.3-3) ... Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4) ... Setting up libpython3.12-stdlib:armhf (3.12.7-3) ... Setting up libkdb5-10t64:armhf (1.21.3-3) ... Setting up python3.12 (3.12.7-3) ... Setting up libhdf5-cpp-103-1t64:armhf (1.10.10+repack-4) ... Setting up libhdf5-fortran-102t64:armhf (1.10.10+repack-4) ... Setting up debhelper (13.20) ... Setting up libkadm5srv-mit12:armhf (1.21.3-3) ... Setting up libhdf5-hl-cpp-100t64:armhf (1.10.10+repack-4) ... Setting up libpython3-stdlib:armhf (3.12.6-1) ... Setting up krb5-multidev:armhf (1.21.3-3) ... Setting up libhdf5-hl-fortran-100t64:armhf (1.10.10+repack-4) ... Setting up python3 (3.12.6-1) ... Setting up libkrb5-dev:armhf (1.21.3-3) ... Setting up libcurl4-openssl-dev:armhf (8.11.0-1) ... Setting up libhdf5-dev (1.10.10+repack-4) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libarmadillo-dev (1:14.0.1+dfsg-2) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/phyx-1.3.2+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../phyx_1.3.2+ds-1_source.changes dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 1.3.2+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds' rm -rf src/phyx.logfile if [ -r src/Makefile ]; then \ /usr/bin/make -C src distclean; \ fi make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src cd src && ./configure --build=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 or later... 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/reproducible-path/phyx-1.3.2+ds/src' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "citations.d" -o "citations.o" "citations.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "log.d" -o "log.o" "log.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "superdouble.d" -o "superdouble.o" "superdouble.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "timer.d" -o "timer.o" "timer.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "sequence.d" -o "sequence.o" "sequence.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_reader.d" -o "seq_reader.o" "seq_reader.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_utils.d" -o "seq_utils.o" "seq_utils.cpp" In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from utils.cpp:6: /usr/include/c++/14/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++/14/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/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_models.d" -o "seq_models.o" "seq_models.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "pairwise_alignment.d" -o "pairwise_alignment.o" "pairwise_alignment.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d" -o "aa2cdn.o" "aa2cdn.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_aa2cdn.d" -o "main_aa2cdn.o" "main_aa2cdn.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "node.d" -o "node.o" "node.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tree.d" -o "tree.o" "tree.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tree_reader.d" -o "tree_reader.o" "tree_reader.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tree_utils.d" -o "tree_utils.o" "tree_utils.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "bd_sim.d" -o "bd_sim.o" "bd_sim.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_bd_sim.d" -o "main_bd_sim.o" "main_bd_sim.cpp" In file included from /usr/include/c++/14/map:62, from bd_sim.cpp:3: /usr/include/c++/14/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++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63: 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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:59:21: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_sample.d" -o "seq_sample.o" "seq_sample.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_boot.d" -o "main_boot.o" "main_boot.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_bp.d" -o "main_bp.o" "main_bp.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "concat.d" -o "concat.o" "concat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_cat.d" -o "main_cat.o" "main_cat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "clean_seq.d" -o "clean_seq.o" "clean_seq.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_clsq.d" -o "main_clsq.o" "main_clsq.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "clean_tree.d" -o "clean_tree.o" "clean_tree.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_cltr.d" -o "main_cltr.o" "main_cltr.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "collapse_tree.d" -o "collapse_tree.o" "collapse_tree.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_colt.d" -o "main_colt.o" "main_colt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "comp_test.d" -o "comp_test.o" "comp_test.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_comp.d" -o "main_comp.o" "main_comp.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_consq.d" -o "main_consq.o" "main_consq.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_fqfilt.d" -o "main_fqfilt.o" "main_fqfilt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "log_manip.d" -o "log_manip.o" "log_manip.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_log.d" -o "main_log.o" "main_log.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_info.d" -o "seq_info.o" "seq_info.cpp" In file included from /usr/include/c++/14/map:62, from seq_info.cpp:2: /usr/include/c++/14/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++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_tree.h: In 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++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63: 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_lssq.d" -o "main_lssq.o" "main_lssq.cpp" 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:272:71: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | 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:273:56: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tree_info.d" -o "tree_info.o" "tree_info.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_lstr.d" -o "main_lstr.o" "main_lstr.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_mono.d" -o "main_mono.o" "main_mono.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_mrca.d" -o "main_mrca.o" "main_mrca.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_mrca_cut.d" -o "main_mrca_cut.o" "main_mrca_cut.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_mrca_name.d" -o "main_mrca_name.o" "main_mrca_name.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_nw.d" -o "main_nw.o" "main_nw.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "polytomy.d" -o "polytomy.o" "polytomy.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_poly.d" -o "main_poly.o" "main_poly.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "recode.d" -o "recode.o" "recode.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_recode.d" -o "main_recode.o" "main_recode.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_revcomp.d" -o "main_revcomp.o" "main_revcomp.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "edlib.d" -o "edlib.o" "edlib.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "relabel.d" -o "relabel.o" "relabel.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rls.d" -o "main_rls.o" "main_rls.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "upgma.d" -o "upgma.o" "upgma.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_upgma.d" -o "main_upgma.o" "main_upgma.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rlt.d" -o "main_rlt.o" "main_rlt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -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++/14/bits/stl_function.h:1435, from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from nj.cpp:1: /usr/include/c++/14/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_nj.d" -o "main_nj.o" "main_nj.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rmk.d" -o "main_rmk.o" "main_rmk.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rms.d" -o "main_rms.o" "main_rms.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rmt.d" -o "main_rmt.o" "main_rmt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_rr.d" -o "main_rr.o" "main_rr.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_s2fa.d" -o "main_s2fa.o" "main_s2fa.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_s2phy.d" -o "main_s2phy.o" "main_s2phy.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "rate_model.d" -o "rate_model.o" "rate_model.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "state_reconstructor.d" -o "state_reconstructor.o" "state_reconstructor.cpp" In file included from /usr/include/c++/14/map:62, from state_reconstructor.cpp:3: /usr/include/c++/14/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++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_nlopt.d" -o "optimize_state_reconstructor_nlopt.o" "optimize_state_reconstructor_nlopt.cpp" In file included from /usr/include/c++/14/map:63: 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++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | 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_periods(Node&)’ at state_reconstructor.cpp:253:66: /usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | 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++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:65, from state_reconstructor.cpp:2: /usr/include/c++/14/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++/14/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++/14/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++/14/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++/14/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = arma::Mat; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, inlined from ‘RateModel::RateModel(const RateModel&)’ at rate_model.h:11:7: /usr/include/c++/14/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++/14/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++/14/bits/stl_uninitialized.h:373:37, 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++/14/bits/stl_vector.h:1624:35, 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++/14/bits/vector.tcc:238:44, inlined from ‘RateModel& RateModel::operator=(const RateModel&)’ at rate_model.h:11:7: /usr/include/c++/14/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/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_periods_nlopt.d" -o "optimize_state_reconstructor_periods_nlopt.o" "optimize_state_reconstructor_periods_nlopt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "branch_segment.d" -o "branch_segment.o" "branch_segment.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "cont_models.d" -o "cont_models.o" "cont_models.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "seq_gen.d" -o "seq_gen.o" "seq_gen.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_seqgen.d" -o "main_seqgen.o" "main_seqgen.cpp" In file included from /usr/include/c++/14/map:62, from /usr/include/armadillo:48, from cont_models.cpp:4: /usr/include/c++/14/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++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63: 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++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | 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++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_ssort.d" -o "main_ssort.o" "main_ssort.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "sstat.d" -o "sstat.o" "sstat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_sstat.d" -o "main_sstat.o" "main_sstat.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_sw.d" -o "main_sw.o" "main_sw.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_t2new.d" -o "main_t2new.o" "main_t2new.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_t2nex.d" -o "main_t2nex.o" "main_t2nex.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tcol.d" -o "main_tcol.o" "main_tcol.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tcomb.d" -o "main_tcomb.o" "main_tcomb.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tgen.d" -o "tgen.o" "tgen.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tgen.d" -o "main_tgen.o" "main_tgen.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tlate.d" -o "tlate.o" "tlate.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tlate.d" -o "main_tlate.o" "main_tlate.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_trt.d" -o "main_trt.o" "main_trt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "tscale.d" -o "tscale.o" "tscale.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_tscale.d" -o "main_tscale.o" "main_tscale.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "vcf_reader.d" -o "vcf_reader.o" "vcf_reader.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_vcf2fa.d" -o "main_vcf2fa.o" "main_vcf2fa.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "bd_fit.d" -o "bd_fit.o" "bd_fit.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_bd_fit.d" -o "main_bd_fit.o" "main_bd_fit.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_contrates.d" -o "main_contrates.o" "main_contrates.cpp" In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from bd_fit.cpp:6: /usr/include/c++/14/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++/14/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++/14/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++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/14/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++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1890 | 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++/14/bits/stl_algo.h:4804:18, inlined from ‘void BDFit::fit_bd()’ at bd_fit.cpp:102:9: /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1905 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1906 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __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++/14/bits/stl_algo.h:1908:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]’ at /usr/include/c++/14/bits/stl_algo.h:4804:18, inlined from ‘void BDFit::fit_bd()’ at bd_fit.cpp:102:9: /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "optimize_cont_models_nlopt.d" -o "optimize_cont_models_nlopt.o" "optimize_cont_models_nlopt.cpp" g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -fmessage-length=0 -MMD -MP -MF "main_strec.d" -o "main_strec.o" "main_strec.cpp" building pxaa2cdn g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxaa2cdn" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize aa2cdn.o main_aa2cdn.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxaa2cdn.1.in > man/pxaa2cdn.1 building pxbdsim g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxbdsim" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize bd_sim.o main_bd_sim.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxbdsim.1.in > man/pxbdsim.1 building pxboot g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxboot" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize seq_sample.o main_boot.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxboot.1.in > man/pxboot.1 building pxbp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxbp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_bp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxbp.1.in > man/pxbp.1 building pxcat g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxcat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize concat.o main_cat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxcat.1.in > man/pxcat.1 building pxclsq g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxclsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize clean_seq.o main_clsq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxclsq.1.in > man/pxclsq.1 building pxcltr g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxcltr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize clean_tree.o main_cltr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxcltr.1.in > man/pxcltr.1 building pxcolt g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxcolt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize collapse_tree.o main_colt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxcolt.1.in > man/pxcolt.1 building pxcomp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize comp_test.o main_comp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxcomp.1.in > man/pxcomp.1 building pxconsq g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxconsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_consq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxconsq.1.in > man/pxconsq.1 building pxfqfilt g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxfqfilt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_fqfilt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxfqfilt.1.in > man/pxfqfilt.1 building pxlog g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxlog" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize log_manip.o main_log.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxlog.1.in > man/pxlog.1 bulding pxlssq g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxlssq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize seq_info.o main_lssq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxlssq.1.in > man/pxlssq.1 building pxlstr g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxlstr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tree_info.o main_lstr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxlstr.1.in > man/pxlstr.1 building pxmono g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxmono" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mono.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxmono.1.in > man/pxmono.1 building pxmrca g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxmrca" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxmrca.1.in > man/pxmrca.1 building pxmrcacut g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxmrcacut" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca_cut.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxmrcacut.1.in > man/pxmrcacut.1 building pxmrcaname g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxmrcaname" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca_name.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxmrcaname.1.in > man/pxmrcaname.1 building pxnw g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxnw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_nw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o building pxpoly g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxpoly" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize polytomy.o main_poly.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxnw.1.in > man/pxnw.1 building pxrecode g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxrecode" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize recode.o main_recode.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxpoly.1.in > man/pxpoly.1 building pxrevcomp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxrevcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_revcomp.o edlib.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrecode.1.in > man/pxrecode.1 building pxrls g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxrls" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize relabel.o main_rls.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrevcomp.1.in > man/pxrevcomp.1 building pxupgma g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxupgma" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize upgma.o main_upgma.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrls.1.in > man/pxrls.1 building pxrlt g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxrlt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize relabel.o main_rlt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxupgma.1.in > man/pxupgma.1 building pxnj g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxnj" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize nj.o main_nj.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrlt.1.in > man/pxrlt.1 building pxrmk g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxrmk" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rmk.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxnj.1.in > man/pxnj.1 building pxrms g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxrms" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rms.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrmk.1.in > man/pxrmk.1 building pxrmt g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxrmt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rmt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrms.1.in > man/pxrms.1 building pxrr g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxrr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrmt.1.in > man/pxrmt.1 building pxs2fa g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxs2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrr.1.in > man/pxrr.1 building pxs2nex g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxs2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxs2fa.1.in > man/pxs2fa.1 building pxs2phy g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxs2phy" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2phy.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxs2nex.1.in > man/pxs2nex.1 building pxseqgen g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -o "pxseqgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_seqgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxssort" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_ssort.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxseqgen.1.in > man/pxseqgen.1 building pxsstat g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxsstat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize sstat.o main_sstat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxssort.1.in > man/pxssort.1 building pxsw g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxsw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_sw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxsstat.1.in > man/pxsstat.1 building pxt2new g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxt2new" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_t2new.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxsw.1.in > man/pxsw.1 building pxt2nex g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxt2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_t2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxt2new.1.in > man/pxt2new.1 building pxtcol g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxtcol" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_tcol.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxt2nex.1.in > man/pxt2nex.1 building pxtcomb g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxtcomb" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_tcomb.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxtcol.1.in > man/pxtcol.1 building pxtgen g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxtgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tgen.o main_tgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxtcomb.1.in > man/pxtcomb.1 building pxtlate g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxtlate" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tlate.o main_tlate.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxtgen.1.in > man/pxtgen.1 building pxtrt g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxtrt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_trt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxtlate.1.in > man/pxtlate.1 building pxtscale g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxtscale" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tscale.o main_tscale.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxtrt.1.in > man/pxtrt.1 cat man/pxtscale.1.in > man/pxtscale.1 building pxvcf2fa g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o "pxvcf2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize vcf_reader.o main_vcf2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o building pxbdfit g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -o "pxbdfit" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize bd_fit.o main_bd_fit.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 pxcontrates g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -o "pxcontrates" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_contrates.o optimize_cont_models_nlopt.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxbdfit.1.in > man/pxbdfit.1 building pxstrec g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/phyx-1.3.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -o "pxstrec" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_strec.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo # -lgfortran cat man/pxcontrates.1.in > man/pxcontrates.1 cat man/pxstrec.1.in > man/pxstrec.1 make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds' cd src && python3 run_tests.py character: 0 character: 1 character: 2 ================= TESTING pxaa2cdn aa2cdn PASSED aa2cdn (remove last codon, all) PASSED aa2cdn (remove stop codon, mixed) PASSED PASSED ================= TESTING pxbdfit yule PASSED birth-death PASSED best PASSED PASSED ================= TESTING pxbdsim taxon stop PASSED time stop PASSED PASSED ================= TESTING pxboot bootstrap PASSED jackknife PASSED PASSED ================= TESTING pxbp node-based PASSED edge-based PASSED PASSED ================= TESTING pxcat PASSED ================= TESTING pxclsq delete proportion PASSED remove empty PASSED min 4 chars per site PASSED info by taxon PASSED PASSED ================= TESTING pxcltr all PASSED labels PASSED knuckles PASSED PASSED ================= TESTING pxcolt probability support PASSED integer support PASSED real support PASSED PASSED ================= TESTING pxcomp PASSED ================= TESTING pxconsq PASSED ================= TESTING pxcontrates PASSED ================= TESTING pxfqfilt PASSED ================= TESTING pxlog count trees PASSED tree log PASSED count parameters PASSED parameter log PASSED summarize parameters PASSED PASSED ================= TESTING pxlssq default PASSED labels PASSED frequencies PASSED indidivual stats PASSED binary data PASSED morph data PASSED fastq PASSED unaliagned PASSED individual missing PASSED PASSED ================= TESTING pxlstr newick PASSED nexus (mulitple) PASSED figtree PASSED polytomy PASSED internal linebreak PASSED terminal labels PASSED PASSED ================= TESTING pxmono PASSED ================= TESTING pxmrca PASSED ================= TESTING pxmrcacut PASSED ================= TESTING pxmrcaname PASSED ================= TESTING pxnj PASSED ================= TESTING pxnw PASSED ================= TESTING pxpoly PASSED ================= TESTING pxrecode RY-coding PASSED MK-coding PASSED SW-coding PASSED PASSED ================= TESTING pxrevcomp PASSED ================= TESTING pxrls name files PASSED regex PASSED ================= TESTING pxrlt name files PASSED regex PASSED ================= TESTING pxrmk PASSED ================= TESTING pxrms command line arg PASSED regex PASSED PASSED ================= TESTING pxrmt command line arg PASSED regex PASSED PASSED ================= TESTING pxrr PASSED ================= TESTING pxs2fa nexus PASSED interleaved nexus PASSED phylip PASSED interleaved phylip PASSED fastq PASSED PASSED ================= TESTING pxs2nex fasta PASSED phylip PASSED interleaved phylip PASSED interleaved nexus PASSED fastq PASSED PASSED ================= TESTING pxs2phy fasta PASSED nexus PASSED interleaved nexus PASSED interleaved phylip PASSED PASSED ================= TESTING pxseqgen PASSED ================= TESTING pxssort sort by id PASSED sort by id rev PASSED sort by length (<) PASSED sort by length (>) PASSED PASSED ================= TESTING pxsstat PASSED ================= TESTING pxstrec PASSED ================= TESTING pxsw PASSED ================= TESTING pxt2new PASSED ================= TESTING pxt2nex PASSED ================= TESTING pxtcol no test for pxtcol ================= TESTING pxtcomb no test for pxtcomb ================= TESTING pxtgen unrooted PASSED rooted PASSED prefix label PASSED PASSED ================= TESTING pxtlate standard PASSED vert mtDNA PASSED PASSED ================= TESTING pxtrt PASSED ================= TESTING pxtscale scale PASSED root height PASSED PASSED ================= TESTING pxupgma PASSED ================= TESTING pxvcf2fa PASSED ================= PASSED PROGRAMS: 47 (102 tests) FAILED PROGRAMS: 0 (0 tests) PROGRAMS WITHOUT TESTS: 2 make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds' mkdir -p /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin dh_auto_install -- PREFIX=/build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr cd src && make -j3 install DESTDIR=/build/reproducible-path/phyx-1.3.2\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/build/reproducible-path/phyx-1.3.2\+ds/debian/phyx/usr make[2]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds/src' mkdir -p /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin && install -m 0755 px* /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin mkdir -p /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/share/man/man1 && install -m 0755 man/px*.1 /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds/src' #echo "#!/usr/bin/python3" > /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin/Phyx_Gui #cat src/Phyx_Gui.py >> /build/reproducible-path/phyx-1.3.2+ds/debian/phyx/usr/bin/Phyx_Gui make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/phyx-1.3.2+ds' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/phyx-1.3.2+ds' dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/pxrmt 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/pxrls 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_1.3.2+ds-1_armhf.deb'. dpkg-deb: building package 'phyx' in '../phyx_1.3.2+ds-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../phyx_1.3.2+ds-1_armhf.buildinfo dpkg-genchanges --build=binary -O../phyx_1.3.2+ds-1_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: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/11703 and its subdirectories I: Current time: Tue Nov 12 17:46:29 -12 2024 I: pbuilder-time-stamp: 1731476789 Wed Nov 13 05:52:23 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32b-armhf-rb.debian.net. Wed Nov 13 05:52:23 UTC 2024 I: Preparing to do remote build '2' on virt32b-armhf-rb.debian.net. Wed Nov 13 06:07:02 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. Wed Nov 13 06:07:07 UTC 2024 I: phyx_1.3.2+ds-1_armhf.changes: Format: 1.8 Date: Sat, 02 Nov 2024 16:22:22 +0100 Source: phyx Binary: phyx phyx-dbgsym Architecture: armhf Version: 1.3.2+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: phyx - UNIX-style phylogenetic analyses on trees and sequences Changes: phyx (1.3.2+ds-1) unstable; urgency=medium . * New upstream version 1.3.2+ds * d/control: build depends on python3:any. The marker :any will allow cross compilation of phyx. * build-more-programs.patch: unfuzz. * i386.patch: delete: applied upstream. * deoptimize.patch: delete: applied upstream. * whatis.patch: refresh to match new versions and timestamps. * hardening.patch: unfuzz. * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: 60ce104285a0755162c16c24b8dca9a91fdc076d 67490688 phyx-dbgsym_1.3.2+ds-1_armhf.deb eed45e1483b57dad16756e313598b7c501c42849 7992 phyx_1.3.2+ds-1_armhf.buildinfo 2435065d2c6db113efe385fe09213dbafed38d52 1858476 phyx_1.3.2+ds-1_armhf.deb Checksums-Sha256: f0ba45d0d4763dc065592c41f8f91ad656f7bcb8ad9a9bec6c2bc78078b39339 67490688 phyx-dbgsym_1.3.2+ds-1_armhf.deb 7f5665406eee198c5da36cca8f75b56d6b0a13c4d63c7c4bcd795c8e7fe95852 7992 phyx_1.3.2+ds-1_armhf.buildinfo cd0b4e04a71de305213350b3f02eda6ff6543dc5ed28b416fc8731d038062ec8 1858476 phyx_1.3.2+ds-1_armhf.deb Files: 6f67af24138212635441cd365a40862e 67490688 debug optional phyx-dbgsym_1.3.2+ds-1_armhf.deb 31063f517256789db4c77409556ad302 7992 science optional phyx_1.3.2+ds-1_armhf.buildinfo a154d44963b403cca6c6a9ea3bc1b687 1858476 science optional phyx_1.3.2+ds-1_armhf.deb Wed Nov 13 06:07:08 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_12-9767.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QANk4eo2/phyx_1.3.2+ds-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QANk4eo2/phyx_1.3.2+ds-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QANk4eo2/phyx_1.3.2+ds-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QANk4eo2/b1/phyx_1.3.2+ds-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.QANk4eo2/b2/phyx_1.3.2+ds-1_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: 0.725s) 0.725s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.459s CPU time consumed: 1.456s Wed Nov 13 06:07:10 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Wed Nov 13 06:07:10 UTC 2024 I: phyx from trixie built successfully and reproducibly on armhf. Wed Nov 13 06:07:11 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Nov 13 06:07:11 UTC 2024 I: Submitting 12K b1/phyx_1.3.2+ds-1_armhf.buildinfo.asc Wed Nov 13 06:07:12 UTC 2024 I: Submitting 12K b2/phyx_1.3.2+ds-1_armhf.buildinfo.asc Wed Nov 13 06:07:13 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Nov 13 06:07:13 UTC 2024 I: Done submitting .buildinfo files. Wed Nov 13 06:07:13 UTC 2024 I: Removing signed phyx_1.3.2+ds-1_armhf.buildinfo.asc files: removed './b1/phyx_1.3.2+ds-1_armhf.buildinfo.asc' removed './b2/phyx_1.3.2+ds-1_armhf.buildinfo.asc'