https://launchpad.net/ubuntu/+source/phyx/1.3+ds-1build1/+build/23845385 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-071 5.4.0-117-generic #132-Ubuntu SMP Thu Jun 2 00:39:06 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_214~560~ubuntu20.04.1 python3-lpbuildd_214~560~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 13 Jun 06:18:05 ntpdate[1807]: adjust time server 10.131.248.1 offset -0.000336 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23845385 --image-type chroot /home/buildd/filecache-default/4d18961cd05542d5def75b14497015b674c37821 Creating target for build PACKAGEBUILD-23845385 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23845385 Starting target for build PACKAGEBUILD-23845385 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23845385 'deb http://ftpmaster.internal/ubuntu kinetic main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-security main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-updates main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-23845385 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23845385 Updating target for build PACKAGEBUILD-23845385 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 Packages [1398 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5721 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 Packages [68.1 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main Translation-en [20.4 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 Packages [345 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/universe Translation-en [190 kB] Fetched 23.1 MB in 2s (11.3 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: util-linux-extra The following packages will be upgraded: adduser apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils cpp-11 dash dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gcc-12-base init init-system-helpers libapt-pkg6.0 libasan6 libatomic1 libbinutils libblkid1 libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgomp1 libgpg-error0 libip4tc2 libitm1 liblsan0 liblzma5 libmount1 libncurses6 libncursesw6 libpng16-16 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lto-disabled-list mount ncurses-base ncurses-bin openssl passwd pinentry-curses readline-common systemd systemd-sysv util-linux xz-utils 79 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 78.8 MB of archives. After this operation, 885 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-files amd64 12.2ubuntu1 [62.6 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 libatomic1 amd64 12.1.0-2ubuntu1 [10.4 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 libubsan1 amd64 12.1.0-2ubuntu1 [969 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main amd64 libquadmath0 amd64 12.1.0-2ubuntu1 [152 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblsan0 amd64 12.1.0-2ubuntu1 [1060 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libitm1 amd64 12.1.0-2ubuntu1 [29.5 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgomp1 amd64 12.1.0-2ubuntu1 [125 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-12-base amd64 12.1.0-2ubuntu1 [18.8 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-s1 amd64 12.1.0-2ubuntu1 [54.2 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcc1-0 amd64 12.1.0-2ubuntu1 [46.6 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++6 amd64 12.1.0-2ubuntu1 [679 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcrypt20 amd64 1.10.1-2ubuntu1 [524 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma5 amd64 5.2.5-2.1 [99.2 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd-sysv amd64 249.11-0ubuntu4 [10.2 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main amd64 libip4tc2 amd64 1.8.7-1ubuntu6 [19.7 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main amd64 libblkid1 amd64 2.38-4ubuntu1 [103 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 libselinux1 amd64 3.4-1 [77.6 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmount1 amd64 2.38-4ubuntu1 [121 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsmartcols1 amd64 2.38-4ubuntu1 [50.8 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main amd64 login amd64 1:4.11.1+dfsg1-2ubuntu1 [183 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux-extra amd64 2.38-4ubuntu1 [83.8 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux amd64 2.38-4ubuntu1 [1069 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main amd64 mount amd64 2.38-4ubuntu1 [114 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage-common all 3.4-1 [9828 B] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsepol2 amd64 3.4-1 [294 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage2 amd64 3.4-1 [91.8 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 passwd amd64 1:4.11.1+dfsg1-2ubuntu1 [765 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 adduser all 3.121ubuntu1 [150 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd amd64 249.11-0ubuntu4 [4517 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsystemd0 amd64 249.11-0ubuntu4 [314 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 libudev1 amd64 249.11-0ubuntu4 [76.1 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapt-pkg6.0 amd64 2.5.0 [896 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg amd64 1.21.8ubuntu1 [1333 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-8 [88.0 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 init-system-helpers all 1.63 [38.7 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 apt amd64 2.5.0 [1370 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 logsave amd64 1.46.5-2ubuntu2 [9914 B] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 libext2fs2 amd64 1.46.5-2ubuntu2 [205 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 e2fsprogs amd64 1.46.5-2ubuntu2 [585 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 init amd64 1.63 [5674 B] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.9 [717 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtinfo6 amd64 6.3+20220423-2 [99.6 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 libuuid1 amd64 2.38-4ubuntu1 [23.2 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcom-err2 amd64 1.46.5-2ubuntu2 [9074 B] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 libss2 amd64 1.46.5-2ubuntu2 [12.3 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 readline-common all 8.1.2-1.2 [53.6 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 libreadline8 amd64 8.1.2-1.2 [153 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsqlite3-0 amd64 3.38.5-1 [646 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libssl3 amd64 3.0.3-5ubuntu3 [1897 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 openssl amd64 3.0.3-5ubuntu3 [1175 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpng16-16 amd64 1.6.37-5 [187 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main amd64 xz-utils amd64 5.2.5-2.1 [83.8 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main amd64 libctf0 amd64 2.38-4ubuntu1 [101 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/main amd64 libctf-nobfd0 amd64 2.38-4ubuntu1 [105 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main amd64 binutils-x86-64-linux-gnu amd64 2.38-4ubuntu1 [2304 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main amd64 libbinutils amd64 2.38-4ubuntu1 [651 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic/main amd64 binutils amd64 2.38-4ubuntu1 [3190 B] Get:65 http://ftpmaster.internal/ubuntu kinetic/main amd64 binutils-common amd64 2.38-4ubuntu1 [221 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main amd64 g++-11 amd64 11.3.0-3ubuntu1 [11.3 MB] Get:67 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++-11-dev amd64 11.3.0-3ubuntu1 [2074 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic/main amd64 libasan6 amd64 11.3.0-3ubuntu1 [2265 kB] Get:69 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11 amd64 11.3.0-3ubuntu1 [20.0 MB] Get:70 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-11-dev amd64 11.3.0-3ubuntu1 [2484 kB] Get:71 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtsan0 amd64 11.3.0-3ubuntu1 [2241 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic/main amd64 cpp-11 amd64 11.3.0-3ubuntu1 [9910 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11-base amd64 11.3.0-3ubuntu1 [20.8 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg-dev all 1.21.8ubuntu1 [1069 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdpkg-perl all 1.21.8ubuntu1 [237 kB] Get:76 http://ftpmaster.internal/ubuntu kinetic/main amd64 lto-disabled-list all 26 [12.4 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfakeroot amd64 1.29-1ubuntu1 [31.1 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic/main amd64 fakeroot amd64 1.29-1ubuntu1 [60.0 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 linux-libc-dev amd64 5.15.0-35.36+22.10.1 [1287 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main amd64 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Setting up libtsan0:amd64 (11.3.0-3ubuntu1) ... Setting up libctf0:amd64 (2.38-4ubuntu1) ... Setting up pinentry-curses (1.2.0-1ubuntu1) ... Setting up cpp-11 (11.3.0-3ubuntu1) ... Setting up libreadline8:amd64 (8.1.2-1.2) ... Setting up e2fsprogs (1.46.5-2ubuntu2) ... Setting up libgcc-11-dev:amd64 (11.3.0-3ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.38-4ubuntu1) ... Setting up binutils (2.38-4ubuntu1) ... Setting up dpkg-dev (1.21.8ubuntu1) ... Setting up libstdc++-11-dev:amd64 (11.3.0-3ubuntu1) ... Setting up gcc-11 (11.3.0-3ubuntu1) ... Setting up g++-11 (11.3.0-3ubuntu1) ... Processing triggers for debianutils (5.7-0.2) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23845385 amd64 kinetic-proposed -c chroot:build-PACKAGEBUILD-23845385 --arch=amd64 --dist=kinetic-proposed --nolog -A phyx_1.3+ds-1build1.dsc Initiating build PACKAGEBUILD-23845385 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-117-generic #132-Ubuntu SMP Thu Jun 2 00:39:06 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-071.buildd +==============================================================================+ | phyx 1.3+ds-1build1 (amd64) Mon, 13 Jun 2022 06:18:23 +0000 | +==============================================================================+ Package: phyx Version: 1.3+ds-1build1 Source Version: 1.3+ds-1build1 Distribution: kinetic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23845385/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/phyx-MJJITE/resolver-iUCXF7' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- phyx_1.3+ds-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/phyx-MJJITE/phyx-1.3+ds' with '<>' I: NOTICE: Log filtering will replace 'build/phyx-MJJITE' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libatlas-cpp-0.6-dev, libarmadillo-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libatlas-cpp-0.6-dev, libarmadillo-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [414 B] Get:5 copy:/<>/apt_archive ./ Packages [498 B] Fetched 1869 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarmadillo-dev libarmadillo11 libarpack2 libarpack2-dev libatlas-cpp-0.6-3 libatlas-cpp-0.6-dev libatlas-cpp-0.6-tools libblas-dev libblas3 libbrotli1 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu71 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libldap-2.5-0 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtool libuchardet0 libxml2 m4 man-db media-types pkg-config po-debconf python3 python3-minimal python3.10 python3.10-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libitpp-dev libatlas-cpp-doc liblapack-doc libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libhdf5-doc libssl-doc libsuperlu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.10-venv python3.10-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarmadillo-dev libarmadillo11 libarpack2 libarpack2-dev libatlas-cpp-0.6-3 libatlas-cpp-0.6-dev libatlas-cpp-0.6-tools libblas-dev libblas3 libbrotli1 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu71 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libldap-2.5-0 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtool libuchardet0 libxml2 m4 man-db media-types pkg-config po-debconf python3 python3-minimal python3.10 python3.10-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. 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kinetic/universe amd64 libnlopt-dev amd64 2.7.1-4build1 [43.6 kB] Get:90 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libnlopt-cxx0 amd64 2.7.1-4build1 [208 kB] Get:91 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libnlopt-cxx-dev amd64 2.7.1-4build1 [9872 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.5 MB in 0s (133 MB/s) Selecting previously unselected package libpython3.10-minimal:amd64. 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Setting up libdebhelper-perl (13.7.1ubuntu1) ... Setting up libbrotli1:amd64 (1.0.9-2build6) ... Setting up libnghttp2-14:amd64 (1.47.0-1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up gettext-base (0.21-6) ... Setting up libnlopt0:amd64 (2.7.1-4build1) ... Setting up file (1:5.41-4) ... Setting up libaec0:amd64 (1.0.6-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-6ubuntu1) ... Setting up libatlas-cpp-0.6-3:amd64 (0.6.4-3) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libsigsegv2:amd64 (2.13-1ubuntu3) ... Setting up libssl-dev:amd64 (3.0.3-5ubuntu3) ... Setting up autopoint (0.21-6) ... Setting up pkg-config (0.29.2-1ubuntu3) ... Setting up libjpeg-turbo8:amd64 (2.1.2-0ubuntu1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-6ubuntu1) ... Setting up libssh-4:amd64 (0.9.6-2build1) ... Setting up libgfortran5:amd64 (12.1.0-2ubuntu1) ... Setting up libnlopt-cxx0:amd64 (2.7.1-4build1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libmpdec3:amd64 (2.5.1-2build2) ... Setting up libsub-override-perl (0.09-2) ... Setting up libnlopt-dev:amd64 (2.7.1-4build1) ... Setting up libatlas-cpp-0.6-tools (0.6.4-3) ... Setting up libelf1:amd64 (0.187-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1) ... Setting up libblas-dev:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.0.6-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu10) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:amd64 (0.187-1) ... Setting up libjpeg-turbo8-dev:amd64 (2.1.2-0ubuntu1) ... Setting up liblapack3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-6) ... Setting up libtool (2.4.7-4) ... Setting up libaec-dev:amd64 (1.0.6-1) ... Setting up libarpack2:amd64 (3.8.0-1) ... Setting up libsuperlu5:amd64 (5.3.0+dfsg1-2) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up libldap-2.5-0:amd64 (2.5.12+dfsg-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3.10-stdlib:amd64 (3.10.5-1) ... Setting up libnlopt-cxx-dev:amd64 (2.7.1-4build1) ... Setting up liblapack-dev:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up libatlas-cpp-0.6-dev:amd64 (0.6.4-3) ... Setting up dwz (0.14-1build2) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libcurl4:amd64 (7.83.1-1ubuntu1) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu10) ... Setting up libsuperlu-dev:amd64 (5.3.0+dfsg1-2) ... Setting up libpython3-stdlib:amd64 (3.10.4-0ubuntu2) ... 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 libarpack2-dev:amd64 (3.8.0-1) ... Setting up python3.10 (3.10.5-1) ... Setting up libarmadillo11 (1:11.1.1+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu10) ... Setting up python3 (3.10.4-0ubuntu2) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up dh-autoreconf (20) ... Setting up libcurl4-openssl-dev:amd64 (7.83.1-1ubuntu1) ... Setting up libhdf5-103-1:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-hl-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up debhelper (13.7.1ubuntu1) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-fortran-102:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-dev (1.10.7+repack-4ubuntu2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libarmadillo-dev (1:11.1.1+dfsg-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-117-generic #132-Ubuntu SMP Thu Jun 2 00:39:06 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.38-4ubuntu1 dpkg-dev_1.21.8ubuntu1 g++-11_11.3.0-3ubuntu1 gcc-11_11.3.0-3ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-3ubuntu1 libstdc++6_12.1.0-2ubuntu1 linux-libc-dev_5.15.0-35.36+22.10.1 Package versions: adduser_3.121ubuntu1 advancecomp_2.1-2.1ubuntu2 apt_2.5.0 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2ubuntu1 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38-4ubuntu1 binutils-common_2.38-4ubuntu1 binutils-x86-64-linux-gnu_2.38-4ubuntu1 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.3.0-3ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79ubuntu1 debhelper_13.7.1ubuntu1 debianutils_5.7-0.2 debugedit_1:5.0-4build1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 dpkg_1.21.8ubuntu1 dpkg-dev_1.21.8ubuntu1 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu2 fakeroot_1.29-1ubuntu1 file_1:5.41-4 findutils_4.8.0-1ubuntu3 g++_4:11.2.0-1ubuntu1 g++-11_11.3.0-3ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.3.0-3ubuntu1 gcc-11-base_11.3.0-3ubuntu1 gcc-12-base_12.1.0-2ubuntu1 gettext_0.21-6 gettext-base_0.21-6 gpg_2.2.27-3ubuntu2 gpg-agent_2.2.27-3ubuntu2 gpgconf_2.2.27-3ubuntu2 gpgv_2.2.27-3ubuntu2 grep_3.7-1build1 groff-base_1.22.4-8build1 gzip_1.10-4ubuntu4 hdf5-helpers_1.10.7+repack-4ubuntu2 hostname_3.23ubuntu2 init_1.63 init-system-helpers_1.63 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapparmor1_3.0.4-2ubuntu2 libapt-pkg6.0_2.5.0 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libarmadillo-dev_1:11.1.1+dfsg-2 libarmadillo11_1:11.1.1+dfsg-2 libarpack2_3.8.0-1 libarpack2-dev_3.8.0-1 libasan6_11.3.0-3ubuntu1 libassuan0_2.5.5-3 libatlas-cpp-0.6-3_0.6.4-3 libatlas-cpp-0.6-dev_0.6.4-3 libatlas-cpp-0.6-tools_0.6.4-3 libatomic1_12.1.0-2ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1build1 libaudit1_1:3.0.7-1build1 libbinutils_2.38-4ubuntu1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38-4ubuntu1 libbrotli1_1.0.9-2build6 libbz2-1.0_1.0.8-5build1 libc-bin_2.35-0ubuntu3 libc-dev-bin_2.35-0ubuntu3 libc6_2.35-0ubuntu3 libc6-dev_2.35-0ubuntu3 libcap-ng0_0.7.9-2.2build3 libcap2_1:2.44-1build3 libcc1-0_12.1.0-2ubuntu1 libcom-err2_1.46.5-2ubuntu2 libcrypt-dev_1:4.4.27-1 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libhdf5-hl-cpp-100_1.10.7+repack-4ubuntu2 libhdf5-hl-fortran-100_1.10.7+repack-4ubuntu2 libhogweed6_3.7.3-1build2 libicu71_71.1-3 libidn2-0_2.3.2-2build1 libip4tc2_1.8.7-1ubuntu6 libisl23_0.24-2build1 libitm1_12.1.0-2ubuntu1 libjpeg-dev_8c-2ubuntu10 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg-turbo8-dev_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu10 libjpeg8-dev_8c-2ubuntu10 libjson-c5_0.16-1 libk5crypto3_1.19.2-2 libkeyutils1_1.6.1-2ubuntu3 libkmod2_29-1ubuntu1 libkrb5-3_1.19.2-2 libkrb5support0_1.19.2-2 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 libldap-2.5-0_2.5.12+dfsg-2ubuntu1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_12.1.0-2ubuntu1 liblz4-1_1.9.3-2build2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4ubuntu1 libmpc3_1.2.1-2build1 libmpdec3_2.5.1-2build2 libmpfr6_4.1.0-3build3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.7.3-1build2 libnghttp2-14_1.47.0-1 libnlopt-cxx-dev_2.7.1-4build1 libnlopt-cxx0_2.7.1-4build1 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perl-modules-5.34_5.34.0-3ubuntu1 pinentry-curses_1.2.0-1ubuntu1 pkg-config_0.29.2-1ubuntu3 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-6ubuntu2 python3_3.10.4-0ubuntu2 python3-minimal_3.10.4-0ubuntu2 python3.10_3.10.5-1 python3.10-minimal_3.10.5-1 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 systemd_249.11-0ubuntu4 systemd-sysv_249.11-0ubuntu4 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-2ubuntu9 zlib1g-dev_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phyx Binary: phyx Architecture: any Version: 1.3+ds-1build1 Maintainer: Ubuntu Developers Uploaders: Andreas Tille Homepage: https://github.com/FePhyFoFum/phyx Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/phyx Vcs-Git: https://salsa.debian.org/med-team/phyx.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libatlas-cpp-0.6-dev, libarmadillo-dev Package-List: phyx deb science optional arch=any Checksums-Sha1: febdde970f6f44c676047f52c6b4625f1db104fc 1187728 phyx_1.3+ds.orig.tar.xz d1ef8be0dd12fad8a8dd0038827aa6cf393a7035 7668 phyx_1.3+ds-1build1.debian.tar.xz Checksums-Sha256: f465a87b9ef03f11a41a47580b28079909e6edbf7b2bda3bab3ae8b70d92f184 1187728 phyx_1.3+ds.orig.tar.xz 514c55b372524a762ca08b71717ee3c30ad6cca83de532f4adb075bca1f98836 7668 phyx_1.3+ds-1build1.debian.tar.xz Files: cc931be75d35c74f22872985a62bfd44 1187728 phyx_1.3+ds.orig.tar.xz 406540fbb723a8dac3db6cda77b36b7a 7668 phyx_1.3+ds-1build1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQJOBAEBCgA4FiEErEg/aN5yj0PyIC/KVo0w8yGyEz0FAmKm1kYaHHN0ZXZlLmxh bmdhc2VrQHVidW50dS5jb20ACgkQVo0w8yGyEz13HxAAxIXrss97gymc3TmeoxFo wsJZKuQd7TbjacxQjTLiaYqTOF0TOVbdAp6/DhD99lMr15W8LdKoCrZHhk1uvZQJ VZg0i3JwLKQxTx4AsnvT6fihpl/ZpmfqfUSLRqVfsoXXm4WlxWUP6kpjezUlF6eo BTb67bReqMqv7xE6ioG8bdaQKsoKnmIFetApCXaVR8orEkn/r+OFQQMJ4z5ayf5/ sAie7l7jOIC9ZG5fT7VjNXoo4qE/kuz5BVeCT+6mv5bgdgp+3wRqlIYFzBw5r6cq xCM9spzshrkc7GsJuzuVXAnfu/GTpMTIfidulQrF9GAAG6DkaI9vE89r95XcJphq qMu37+Ah3/63JBNokmzHZlcKthp/cdnG0E6tGZ75a6Z3GDRIrH2oH5t0CqsSwpiV BC1DmdZO2aMGS9BtyXqdOsYOJoUDE2qlU3ovvYzTa/SsbhmS84PJb6k0gIhowS3X hk0/DVEkqsqHVZTztWRuklL9ZsR5bC/7IYTJzjZcGWcaZMzIdiETdwU5pVyoeR88 nEkEEpw7vhyVkAOFz0aAnmk6VTXKMKQQzkGAonwHrAGkkcgS+pGe3K90sXpcF4X8 VazY6Koz7XL1SWnOTrxkEKcGCu+nG82ln2UwvC8bmHJZ41aBBXILhQY0UIhbf/HY oJ3UHEi5pr63ea2f1UKPkqY= =VH4v -----END PGP SIGNATURE----- gpgv: Signature made Mon Jun 13 06:16:38 2022 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./phyx_1.3+ds-1build1.dsc dpkg-source: info: extracting phyx in /<> dpkg-source: info: unpacking phyx_1.3+ds.orig.tar.xz dpkg-source: info: unpacking phyx_1.3+ds-1build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying build-more-programs.patch dpkg-source: info: applying i386.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-23845385 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23845385 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23845385 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 1.3+ds-1build1 dpkg-buildpackage: info: source distribution kinetic dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf src/phyx.logfile if [ -r src/Makefile ]; then \ /usr/bin/make -C src distclean; \ fi make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src cd src && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for fabs in -lm... yes checking for nlopt_version in -lnlopt... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for nlopt.h... yes checking for library containing wrapper_sgesv_... -larmadillo checking for fenv.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for size_t... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for GNU libc compatible malloc... yes checking for working strtod... yes checking for floor... yes checking for pow... yes checking for sqrt... yes configure: creating ./config.status config.status: creating Makefile config.status: creating config.h dh_auto_build -O--sourcedirectory=src cd src && make -j4 make[1]: Entering directory '/<>/src' g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "citations.d" -o "citations.o" "citations.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "log.d" -o "log.o" "log.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "superdouble.d" -o "superdouble.o" "superdouble.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "timer.d" -o "timer.o" "timer.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "sequence.d" -o "sequence.o" "sequence.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_reader.d" -o "seq_reader.o" "seq_reader.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_utils.d" -o "seq_utils.o" "seq_utils.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_models.d" -o "seq_models.o" "seq_models.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "pairwise_alignment.d" -o "pairwise_alignment.o" "pairwise_alignment.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d" -o "aa2cdn.o" "aa2cdn.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_aa2cdn.d" -o "main_aa2cdn.o" "main_aa2cdn.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "node.d" -o "node.o" "node.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree.d" -o "tree.o" "tree.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_reader.d" -o "tree_reader.o" "tree_reader.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_utils.d" -o "tree_utils.o" "tree_utils.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "bd_sim.d" -o "bd_sim.o" "bd_sim.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bd_sim.d" -o "main_bd_sim.o" "main_bd_sim.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_sample.d" -o "seq_sample.o" "seq_sample.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_boot.d" -o "main_boot.o" "main_boot.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bp.d" -o "main_bp.o" "main_bp.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "concat.d" -o "concat.o" "concat.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_cat.d" -o "main_cat.o" "main_cat.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "clean_seq.d" -o "clean_seq.o" "clean_seq.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_clsq.d" -o "main_clsq.o" "main_clsq.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "clean_tree.d" -o "clean_tree.o" "clean_tree.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_cltr.d" -o "main_cltr.o" "main_cltr.cpp" g++ -g -O2 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-Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rr.d" -o "main_rr.o" "main_rr.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2fa.d" -o "main_s2fa.o" "main_s2fa.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2phy.d" -o "main_s2phy.o" "main_s2phy.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "rate_model.d" -o "rate_model.o" "rate_model.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "state_reconstructor.d" -o "state_reconstructor.o" "state_reconstructor.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_nlopt.d" -o "optimize_state_reconstructor_nlopt.o" "optimize_state_reconstructor_nlopt.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_periods_nlopt.d" -o "optimize_state_reconstructor_periods_nlopt.o" "optimize_state_reconstructor_periods_nlopt.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "branch_segment.d" -o "branch_segment.o" "branch_segment.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "cont_models.d" -o "cont_models.o" "cont_models.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_gen.d" -o "seq_gen.o" "seq_gen.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_seqgen.d" -o "main_seqgen.o" "main_seqgen.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_ssort.d" -o "main_ssort.o" "main_ssort.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "sstat.d" -o "sstat.o" "sstat.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_sstat.d" -o "main_sstat.o" "main_sstat.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_sw.d" -o "main_sw.o" "main_sw.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_t2new.d" -o "main_t2new.o" "main_t2new.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_t2nex.d" -o "main_t2nex.o" "main_t2nex.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tcol.d" -o "main_tcol.o" "main_tcol.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tcomb.d" -o "main_tcomb.o" "main_tcomb.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tgen.d" -o "tgen.o" "tgen.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tgen.d" -o "main_tgen.o" "main_tgen.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tlate.d" -o "tlate.o" "tlate.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tlate.d" -o "main_tlate.o" "main_tlate.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_trt.d" -o "main_trt.o" "main_trt.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tscale.d" -o "tscale.o" "tscale.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tscale.d" -o "main_tscale.o" "main_tscale.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "vcf_reader.d" -o "vcf_reader.o" "vcf_reader.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_vcf2fa.d" -o "main_vcf2fa.o" "main_vcf2fa.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "bd_fit.d" -o "bd_fit.o" "bd_fit.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bd_fit.d" -o "main_bd_fit.o" "main_bd_fit.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_contrates.d" -o "main_contrates.o" "main_contrates.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "optimize_cont_models_nlopt.d" -o "optimize_cont_models_nlopt.o" "optimize_cont_models_nlopt.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_strec.d" -o "main_strec.o" "main_strec.cpp" building pxaa2cdn g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxaa2cdn" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math aa2cdn.o main_aa2cdn.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxaa2cdn.1.in > man/pxaa2cdn.1 building pxbdsim g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxbdsim" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math bd_sim.o main_bd_sim.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now building pxboot g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxboot" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math seq_sample.o main_boot.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now building pxbp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxbp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_bp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxbdsim.1.in > man/pxbdsim.1 building pxcat g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math concat.o main_cat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxboot.1.in > man/pxboot.1 building pxclsq g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxclsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math clean_seq.o main_clsq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxbp.1.in > man/pxbp.1 building pxcltr g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcltr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math clean_tree.o main_cltr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now building pxcolt g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcolt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math collapse_tree.o main_colt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxcat.1.in > man/pxcat.1 building pxcomp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math comp_test.o main_comp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxcltr.1.in > man/pxcltr.1 building pxconsq g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxconsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_consq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxclsq.1.in > man/pxclsq.1 building pxfqfilt g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxfqfilt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_fqfilt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxcolt.1.in > man/pxcolt.1 building pxlog g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlog" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math log_manip.o main_log.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxfqfilt.1.in > man/pxfqfilt.1 bulding pxlssq g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlssq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math seq_info.o main_lssq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxcomp.1.in > man/pxcomp.1 building pxlstr g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlstr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tree_info.o main_lstr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxlog.1.in > man/pxlog.1 building pxmono g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmono" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mono.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxconsq.1.in > man/pxconsq.1 building pxmrca g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrca" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxlssq.1.in > man/pxlssq.1 building pxmrcacut g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrcacut" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca_cut.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxlstr.1.in > man/pxlstr.1 building pxmrcaname g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrcaname" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca_name.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxmono.1.in > man/pxmono.1 building pxnw g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxnw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_nw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxmrca.1.in > man/pxmrca.1 building pxpoly g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxpoly" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math polytomy.o main_poly.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxmrcacut.1.in > man/pxmrcacut.1 building pxrecode g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrecode" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math recode.o main_recode.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxmrcaname.1.in > man/pxmrcaname.1 building pxrevcomp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrevcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_revcomp.o edlib.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxpoly.1.in > man/pxpoly.1 building pxrls g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrls" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math relabel.o main_rls.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxnw.1.in > man/pxnw.1 building pxupgma g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxupgma" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math upgma.o main_upgma.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxrevcomp.1.in > man/pxrevcomp.1 building pxrlt g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrlt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math relabel.o main_rlt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxrecode.1.in > man/pxrecode.1 building pxnj g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxnj" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math nj.o main_nj.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxrls.1.in > man/pxrls.1 building pxrmk g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrmk" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rmk.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxupgma.1.in > man/pxupgma.1 building pxrms g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrms" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rms.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxrlt.1.in > man/pxrlt.1 building pxrmt g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrmt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rmt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxnj.1.in > man/pxnj.1 building pxrr g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxrmk.1.in > man/pxrmk.1 building pxs2fa g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxrms.1.in > man/pxrms.1 building pxs2nex g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxs2fa.1.in > man/pxs2fa.1 building pxs2phy g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2phy" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2phy.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxrmt.1.in > man/pxrmt.1 building pxseqgen g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -o "pxseqgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_seqgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxrr.1.in > man/pxrr.1 building pxssort g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxssort" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_ssort.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxs2nex.1.in > man/pxs2nex.1 building pxsstat g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxsstat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math sstat.o main_sstat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxs2phy.1.in > man/pxs2phy.1 building pxsw g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxsw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_sw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxseqgen.1.in > man/pxseqgen.1 building pxt2new g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxt2new" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_t2new.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxssort.1.in > man/pxssort.1 building pxt2nex g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxt2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_t2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxt2new.1.in > man/pxt2new.1 building pxtcol g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtcol" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_tcol.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxsstat.1.in > man/pxsstat.1 building pxtcomb g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtcomb" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_tcomb.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxt2nex.1.in > man/pxt2nex.1 building pxtgen g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tgen.o main_tgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxsw.1.in > man/pxsw.1 building pxtlate g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtlate" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tlate.o main_tlate.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxtcol.1.in > man/pxtcol.1 building pxtrt g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtrt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_trt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxtgen.1.in > man/pxtgen.1 building pxtscale g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtscale" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tscale.o main_tscale.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxtcomb.1.in > man/pxtcomb.1 building pxvcf2fa g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxvcf2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math vcf_reader.o main_vcf2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now cat man/pxvcf2fa.1.in > man/pxvcf2fa.1 building pxbdfit g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -o "pxbdfit" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math bd_fit.o main_bd_fit.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxtlate.1.in > man/pxtlate.1 building pxcontrates g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -o "pxcontrates" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_contrates.o optimize_cont_models_nlopt.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxtscale.1.in > man/pxtscale.1 building pxstrec g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -o "pxstrec" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_strec.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo # -lgfortran cat man/pxtrt.1.in > man/pxtrt.1 cat man/pxbdfit.1.in > man/pxbdfit.1 cat man/pxcontrates.1.in > man/pxcontrates.1 cat man/pxstrec.1.in > man/pxstrec.1 make[1]: Leaving directory '/<>/src' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd src && python3 run_tests.py character: 0 character: 1 character: 2 ================= TESTING pxaa2cdn PASSED ================= TESTING pxbdfit yule PASSED birth-death PASSED best PASSED PASSED ================= TESTING pxbdsim taxon stop PASSED time stop PASSED PASSED ================= TESTING pxboot bootstrap PASSED jackknife PASSED PASSED ================= TESTING pxbp PASSED ================= TESTING pxcat PASSED ================= TESTING pxclsq delete sites PASSED info by taxon PASSED PASSED ================= TESTING pxcltr all PASSED labels PASSED knuckles PASSED PASSED ================= TESTING pxcolt probability support PASSED integer support PASSED real support PASSED PASSED ================= TESTING pxcomp PASSED ================= TESTING pxconsq PASSED ================= TESTING pxcontrates PASSED ================= TESTING pxfqfilt PASSED ================= TESTING pxlog count trees PASSED tree log PASSED count parameters PASSED parameter log PASSED PASSED ================= TESTING pxlssq default PASSED labels PASSED frequencies PASSED indidivual stats PASSED binary data PASSED morph data PASSED fastq PASSED unaliagned PASSED individual missing PASSED PASSED ================= TESTING pxlstr newick PASSED nexus (mulitple) PASSED figtree PASSED polytomy PASSED internal linebreak PASSED PASSED ================= TESTING pxmono PASSED ================= TESTING pxmrca PASSED ================= TESTING pxmrcacut PASSED ================= TESTING pxmrcaname PASSED ================= TESTING pxnj PASSED ================= TESTING pxnw PASSED ================= TESTING pxpoly PASSED ================= TESTING pxrecode RY-coding PASSED MK-coding PASSED SW-coding PASSED PASSED ================= TESTING pxrevcomp PASSED ================= TESTING pxrls PASSED ================= TESTING pxrlt PASSED ================= TESTING pxrmk PASSED ================= TESTING pxrms command line arg PASSED regex PASSED PASSED ================= TESTING pxrmt command line arg PASSED regex PASSED PASSED ================= TESTING pxrr PASSED ================= TESTING pxs2fa nexus PASSED interleaved nexus PASSED phylip PASSED interleaved phylip PASSED fastq PASSED PASSED ================= TESTING pxs2nex fasta PASSED phylip PASSED interleaved phylip PASSED interleaved nexus PASSED fastq PASSED PASSED ================= TESTING pxs2phy fasta PASSED nexus PASSED interleaved nexus PASSED interleaved phylip PASSED PASSED ================= TESTING pxseqgen PASSED ================= TESTING pxssort sort by id PASSED sort by id rev PASSED sort by length (<) PASSED sort by length (>) PASSED PASSED ================= TESTING pxsstat PASSED ================= TESTING pxstrec PASSED ================= TESTING pxsw PASSED ================= TESTING pxt2new PASSED ================= TESTING pxt2nex PASSED ================= TESTING pxtcol no test for pxtcol ================= TESTING pxtcomb no test for pxtcomb ================= TESTING pxtgen unrooted PASSED rooted PASSED prefix label PASSED PASSED ================= TESTING pxtlate standard PASSED vert mtDNA PASSED PASSED ================= TESTING pxtrt PASSED ================= TESTING pxtscale scale PASSED root height PASSED PASSED ================= TESTING pxupgma PASSED ================= TESTING pxvcf2fa PASSED ================= PASSED PROGRAMS: 47 (93 tests) FAILED PROGRAMS: 0 (0 tests) PROGRAMS WITHOUT TESTS: 2 make[1]: Leaving directory '/<>' 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 '/<>' mkdir -p /<>/debian/phyx/usr/bin dh_auto_install -- PREFIX=/<>/debian/phyx/usr cd src && make -j4 install DESTDIR=/<>/phyx-1.3\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/<>/phyx-1.3\+ds/debian/phyx/usr make[2]: Entering directory '/<>/src' mkdir -p /<>/debian/phyx/usr/bin && install -m 0755 px* /<>/debian/phyx/usr/bin mkdir -p /<>/debian/phyx/usr/share/man/man1 && install -m 0755 man/px*.1 /<>/debian/phyx/usr/share/man/man1 make[2]: Leaving directory '/<>/src' #echo "#!/usr/bin/python3" > /<>/debian/phyx/usr/bin/Phyx_Gui #cat src/Phyx_Gui.py >> /<>/debian/phyx/usr/bin/Phyx_Gui make[1]: Leaving directory '/<>' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src debugedit: debian/phyx/usr/bin/pxsw: Unknown DWARF DW_FORM_0x1f20 18cd381ea4f0d4086c68ca99fa37446f453fd7c6 debugedit: debian/phyx/usr/bin/pxsstat: Unknown DWARF DW_FORM_0x1f20 b197267dd9d19fc7a04e70cbfc9b375be775a5f1 debugedit: debian/phyx/usr/bin/pxtgen: Unknown DWARF DW_FORM_0x1f21 3f6a01393a3f0ec61e00924cce05a6c4d9196027 debugedit: debian/phyx/usr/bin/pxmrca: Unknown DWARF DW_FORM_0x1f21 481cbd403cfe598617f845ff7c43260592217abb debugedit: debian/phyx/usr/bin/pxcltr: Unknown DWARF DW_FORM_0x1f21 0a661e6898fe2f60e36f6bbc1a2e4b79e5604580 debugedit: debian/phyx/usr/bin/pxs2fa: Unknown DWARF DW_FORM_0x1f20 0762aa27f9509e2e2a78d97cffbb8c44704a4cad debugedit: debian/phyx/usr/bin/pxbp: Unknown DWARF DW_FORM_0x1f21 632ff7192dc0f38ca70bd4e0418ac5ef022df1da debugedit: debian/phyx/usr/bin/pxcat: Unknown DWARF DW_FORM_0x1f21 d7e529872cfc5875842a08fd5e4bc97fa4b908c0 debugedit: debian/phyx/usr/bin/pxrls: Unknown DWARF DW_FORM_0x1f21 4e29f9eca52866c1529978316367c0ec8be3199b debugedit: debian/phyx/usr/bin/pxcontrates: Unknown DWARF DW_FORM_0x1f21 121bfdf53e2b74ca2cb82ba8e9c28bbda3417d89 debugedit: debian/phyx/usr/bin/pxlstr: Unknown DWARF DW_FORM_0x1f21 6e2d0590d15e80836b98c7465235d213078b96f5 debugedit: debian/phyx/usr/bin/pxrlt: Unknown DWARF DW_FORM_0x1f21 319e1f872949143ec0ebff85d18eb187ee12aef1 debugedit: debian/phyx/usr/bin/pxt2new: Unknown DWARF DW_FORM_0x1f21 6e1a5a3301329358b596259211ccc2f7dd5bf331 debugedit: debian/phyx/usr/bin/pxboot: Unknown DWARF DW_FORM_0x1f21 f86ee73dfd3a81c5a084a6d18af5ef4665d0be20 debugedit: debian/phyx/usr/bin/pxcolt: Unknown DWARF DW_FORM_0x1f21 cd244c0f3425340fffff771be9ae06c6ba8e43f8 debugedit: debian/phyx/usr/bin/pxpoly: Unknown DWARF DW_FORM_0x1f21 50e0e9987a84dd43788ad56a9c6b6c5dee730957 debugedit: debian/phyx/usr/bin/pxclsq: Unknown DWARF DW_FORM_0x1f20 04b7d6355ef555e738e7d522a008a1a2669356ca debugedit: debian/phyx/usr/bin/pxfqfilt: Unknown DWARF DW_FORM_0x1f21 51e2c996cc4d4f43efea276eaf3e4ea14ce1493f debugedit: debian/phyx/usr/bin/pxbdsim: Unknown DWARF DW_FORM_0x1f21 28e3f7c65b9e8a0218095f5c7ba21dd95587fd16 debugedit: debian/phyx/usr/bin/pxlssq: Unknown DWARF DW_FORM_0x1f20 d6fd28fef4761556e7bc8a147c04df49578e87c4 debugedit: debian/phyx/usr/bin/pxs2phy: Unknown DWARF DW_FORM_0x1f20 74d0d1ebb41d46412372886ba7daa2ffb84fc2e8 debugedit: debian/phyx/usr/bin/pxtcol: Unknown DWARF DW_FORM_0x1f21 76fceab84befe6515c30ad7928eaebfef572d3ab debugedit: debian/phyx/usr/bin/pxrevcomp: Unknown DWARF DW_FORM_0x1f21 99d765ff48ba2dfcb3bb0122cf89cc3940022c81 debugedit: debian/phyx/usr/bin/pxbdfit: Unknown DWARF DW_FORM_0x1f21 b0dcf2d41069f2d510cfeb1c03a1d1e92c446ce4 debugedit: debian/phyx/usr/bin/pxstrec: Unknown DWARF DW_FORM_0x1f21 c4fc97083f607fe551c7d2b849d06ae5010afaef debugedit: debian/phyx/usr/bin/pxt2nex: Unknown DWARF DW_FORM_0x1f21 64c30b5f4fc5ba0ea1be657bed771666af5a3a9a debugedit: debian/phyx/usr/bin/pxtrt: Unknown DWARF DW_FORM_0x1f21 37ee21cb76414c2cdae333abb39016b42f9d6ffe debugedit: debian/phyx/usr/bin/pxlog: Unknown DWARF DW_FORM_0x1f21 8dc850afc97f03cb7ad3733bb62cb99d84aafabd debugedit: debian/phyx/usr/bin/pxcomp: Unknown DWARF DW_FORM_0x1f21 eb514894166dd616a9d5d08eecba39aec704c27c debugedit: debian/phyx/usr/bin/pxrr: Unknown DWARF DW_FORM_0x1f21 95f89e99244aa5369726a573fd2362a6f8af525c debugedit: debian/phyx/usr/bin/pxrms: Unknown DWARF DW_FORM_0x1f20 61533c77a425cd92bece9cd74247f0d4f83f98b5 debugedit: debian/phyx/usr/bin/pxrecode: Unknown DWARF DW_FORM_0x1f21 95dc3c3ae734b8afe0522fc4d74bfaed06c5dd83 debugedit: debian/phyx/usr/bin/pxnj: Unknown DWARF DW_FORM_0x1f21 ccb6933f769921e4df77f2778dd72f3b1db428b7 debugedit: debian/phyx/usr/bin/pxrmk: Unknown DWARF DW_FORM_0x1f21 b603ba32eaec6a33da84b7c0557f333091bcc58a debugedit: debian/phyx/usr/bin/pxssort: Unknown DWARF DW_FORM_0x1f20 d21af197e89c2552c009f18a80977ef820d45f37 debugedit: debian/phyx/usr/bin/pxmrcacut: Unknown DWARF DW_FORM_0x1f21 7e564ace906d53580fa3ea595a2d3b9cb9541f83 debugedit: debian/phyx/usr/bin/pxmrcaname: Unknown DWARF DW_FORM_0x1f21 e393d892d0b5dfe36a54e296839784e3375e10a4 debugedit: debian/phyx/usr/bin/pxtcomb: Unknown DWARF DW_FORM_0x1f21 c31c54172613c4a8204763e6b6bb915919a7ca58 debugedit: debian/phyx/usr/bin/pxupgma: Unknown DWARF DW_FORM_0x1f20 a983a0827adb5da2e0b4c3ebf594c4c188210b79 debugedit: debian/phyx/usr/bin/pxmono: Unknown DWARF DW_FORM_0x1f21 5ab4d7738d34128e60372a200fb3ca28faa60c54 debugedit: debian/phyx/usr/bin/pxnw: Unknown DWARF DW_FORM_0x1f20 621889993af485c6c86ae2649c2a0b3600ffe2ff debugedit: debian/phyx/usr/bin/pxs2nex: Unknown DWARF DW_FORM_0x1f20 85f20edc3c6b7e33232440d26377d5ee6f320493 debugedit: debian/phyx/usr/bin/pxtlate: Unknown DWARF DW_FORM_0x1f20 1fc9141ecec658a204dfcc0ce79f22257727460c debugedit: debian/phyx/usr/bin/pxconsq: Unknown DWARF DW_FORM_0x1f20 1da0bb4315352d334ac43b4f5baee221b02dd6be debugedit: debian/phyx/usr/bin/pxtscale: Unknown DWARF DW_FORM_0x1f21 3c500a704d7b6c3bf651fa82351d5a342ea2256d debugedit: debian/phyx/usr/bin/pxseqgen: Unknown DWARF DW_FORM_0x1f21 6589f2641442057e0eb6a57108ea9b624c42f657 debugedit: debian/phyx/usr/bin/pxvcf2fa: Unknown DWARF DW_FORM_0x1f21 8e0245164225aa46587316bd7c961999e39a2880 debugedit: debian/phyx/usr/bin/pxrmt: Unknown DWARF DW_FORM_0x1f21 aa9758965586789d0bd924c8ba2ac8ca7ca54dd2 debugedit: debian/phyx/usr/bin/pxaa2cdn: Unknown DWARF DW_FORM_0x1f21 08895b0ad4ba08e87ff0bda39762f270ea8ad850 dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing phyx (in debian/phyx); do_strip: , oemstrip: pkgstriptranslations: processing phyx-dbgsym (in debian/.debhelper/phyx/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/phyx/DEBIAN/control, package phyx, directory debian/phyx pkgstripfiles: processing control file: debian/.debhelper/phyx/dbgsym-root/DEBIAN/control, package phyx-dbgsym, directory debian/.debhelper/phyx/dbgsym-root dpkg-deb: building package 'phyx-dbgsym' in 'debian/.debhelper/scratch-space/build-phyx/phyx-dbgsym_1.3+ds-1build1_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package phyx ... pkgstripfiles: No PNG files. dpkg-deb: building package 'phyx' in '../phyx_1.3+ds-1build1_amd64.deb'. Renaming phyx-dbgsym_1.3+ds-1build1_amd64.deb to phyx-dbgsym_1.3+ds-1build1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../phyx_1.3+ds-1build1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../phyx_1.3+ds-1build1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-06-13T06:20:17Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phyx_1.3+ds-1build1_amd64.changes: ---------------------------------- Format: 1.8 Date: Mon, 13 Jun 2022 06:16:37 +0000 Source: phyx Binary: phyx Built-For-Profiles: noudeb Architecture: amd64 Version: 1.3+ds-1build1 Distribution: kinetic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: phyx - UNIX-style phylogenetic analyses on trees and sequences Changes: phyx (1.3+ds-1build1) kinetic; urgency=medium . * No-change rebuild against libarmadillo11 Checksums-Sha1: 4b20dcff5591d83889e0629722bc580863315fd1 22354940 phyx-dbgsym_1.3+ds-1build1_amd64.ddeb 6a29bde430dc5c1336837988da35087cf5ee8b85 8058 phyx_1.3+ds-1build1_amd64.buildinfo b8ec2c83ffe3b5471578f6a5af0a7a0e0fe30792 1508880 phyx_1.3+ds-1build1_amd64.deb Checksums-Sha256: 02f56b273c683cba9021f30cbf34e02c553d4e5f89c89d1453cd0b6faddf7495 22354940 phyx-dbgsym_1.3+ds-1build1_amd64.ddeb 14c8781cc9e00d7a4108718535e1bfda55cb051226bd4287766a5e6f72449444 8058 phyx_1.3+ds-1build1_amd64.buildinfo eff70dedf847f92f0d1730df1f6417e237b11d3b3dd677b6f9b7049b04b2bada 1508880 phyx_1.3+ds-1build1_amd64.deb Files: f0af400bcf694bf89cbfaa6b180cc883 22354940 debug optional phyx-dbgsym_1.3+ds-1build1_amd64.ddeb a41a7c21152ab02929f73379ab9849e4 8058 science optional phyx_1.3+ds-1build1_amd64.buildinfo 893ee71349286dff2eeb2e3b79e42576 1508880 science optional phyx_1.3+ds-1build1_amd64.deb Original-Maintainer: Debian Med Packaging Team /<>/phyx_1.3+ds-1build1_amd64.changes.new could not be renamed to /<>/phyx_1.3+ds-1build1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phyx Binary: phyx phyx-dbgsym Architecture: amd64 Version: 1.3+ds-1build1 Checksums-Md5: f0af400bcf694bf89cbfaa6b180cc883 22354940 phyx-dbgsym_1.3+ds-1build1_amd64.ddeb 893ee71349286dff2eeb2e3b79e42576 1508880 phyx_1.3+ds-1build1_amd64.deb Checksums-Sha1: 4b20dcff5591d83889e0629722bc580863315fd1 22354940 phyx-dbgsym_1.3+ds-1build1_amd64.ddeb b8ec2c83ffe3b5471578f6a5af0a7a0e0fe30792 1508880 phyx_1.3+ds-1build1_amd64.deb Checksums-Sha256: 02f56b273c683cba9021f30cbf34e02c553d4e5f89c89d1453cd0b6faddf7495 22354940 phyx-dbgsym_1.3+ds-1build1_amd64.ddeb eff70dedf847f92f0d1730df1f6417e237b11d3b3dd677b6f9b7049b04b2bada 1508880 phyx_1.3+ds-1build1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Mon, 13 Jun 2022 06:20:17 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2ubuntu1), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38-4ubuntu1), binutils-common (= 2.38-4ubuntu1), binutils-x86-64-linux-gnu (= 2.38-4ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-3ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8), debconf (= 1.5.79ubuntu1), debhelper (= 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2:8.39-14), libperl5.34 (= 5.34.0-3ubuntu1), libpipeline1 (= 1.5.6-1), libpsl5 (= 0.21.0-1.2build2), libpython3-stdlib (= 3.10.4-0ubuntu2), libpython3.10-minimal (= 3.10.5-1), libpython3.10-stdlib (= 3.10.5-1), libquadmath0 (= 12.1.0-2ubuntu1), libreadline8 (= 8.1.2-1.2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-6ubuntu1), libsasl2-modules-db (= 2.1.28+dfsg-6ubuntu1), libseccomp2 (= 2.5.4-1ubuntu1), libselinux1 (= 3.4-1), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.38-4ubuntu1), libsqlite3-0 (= 3.38.5-1), libssh-4 (= 0.9.6-2build1), libssl-dev (= 3.0.3-5ubuntu3), libssl3 (= 3.0.3-5ubuntu3), libstdc++-11-dev (= 11.3.0-3ubuntu1), libstdc++6 (= 12.1.0-2ubuntu1), libsub-override-perl (= 0.09-2), libsuperlu-dev (= 5.3.0+dfsg1-2), libsuperlu5 (= 5.3.0+dfsg1-2), libsystemd0 (= 249.11-0ubuntu4), libsz2 (= 1.0.6-1), libtasn1-6 (= 4.18.0-4build1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-3ubuntu1), libubsan1 (= 12.1.0-2ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 249.11-0ubuntu4), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libxml2 (= 2.9.14+dfsg-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-35.36+22.10.1), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 26), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3), media-types (= 8.0.0), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), pkg-config (= 0.29.2-1ubuntu3), po-debconf (= 1.0.21+nmu1), python3 (= 3.10.4-0ubuntu2), python3-minimal (= 3.10.4-0ubuntu2), python3.10 (= 3.10.5-1), python3.10-minimal (= 3.10.5-1), readline-common (= 8.1.2-1.2), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1655100997" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phyx_1.3+ds-1build1_amd64.deb ----------------------------- new Debian package, version 2.0. size 1508880 bytes: control archive=5039 bytes. 1427 bytes, 23 lines control 12472 bytes, 175 lines md5sums Package: phyx Version: 1.3+ds-1build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 6776 Depends: libarmadillo11 (>= 1:11.1.1+dfsg), libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libgomp1 (>= 4.9), libnlopt0 (>= 2.6.1), libstdc++6 (>= 11), python3 Section: science Priority: optional Homepage: https://github.com/FePhyFoFum/phyx Description: UNIX-style phylogenetic analyses on trees and sequences phyx provides a convenient, lightweight and inclusive toolkit consisting of programs spanning the wide breadth of programs utilized by researchers performing phylogenomic analyses. Modeled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams. A result of this stream-centric approach is that, for most programs, only a single sequence or tree is in memory at any moment. Thus, large datasets can be processed with minimal memory requirements. phyx’s ever-growing complement of programs consists of over 35 programs focused on exploring, manipulating, analyzing and simulating phylogenetic objects (alignments, trees and MCMC logs). As with standard Unix command line tools, these programs can be piped (together with non-phyx tools), allowing the easy construction of efficient analytical pipelines. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2022-06-13 06:16 ./ drwxr-xr-x root/root 0 2022-06-13 06:16 ./usr/ drwxr-xr-x root/root 0 2022-06-13 06:16 ./usr/bin/ -rwxr-xr-x root/root 113120 2022-06-13 06:16 ./usr/bin/pxaa2cdn -rwxr-xr-x root/root 76288 2022-06-13 06:16 ./usr/bin/pxbdfit -rwxr-xr-x root/root 55792 2022-06-13 06:16 ./usr/bin/pxbdsim -rwxr-xr-x root/root 100840 2022-06-13 06:16 ./usr/bin/pxboot -rwxr-xr-x root/root 100840 2022-06-13 06:16 ./usr/bin/pxbp -rwxr-xr-x root/root 104928 2022-06-13 06:16 ./usr/bin/pxcat -rwxr-xr-x root/root 104936 2022-06-13 06:16 ./usr/bin/pxclsq -rwxr-xr-x root/root 59872 2022-06-13 06:16 ./usr/bin/pxcltr -rwxr-xr-x root/root 59880 2022-06-13 06:16 ./usr/bin/pxcolt -rwxr-xr-x root/root 96736 2022-06-13 06:16 ./usr/bin/pxcomp -rwxr-xr-x root/root 92640 2022-06-13 06:16 ./usr/bin/pxconsq -rwxr-xr-x root/root 170496 2022-06-13 06:16 ./usr/bin/pxcontrates -rwxr-xr-x root/root 39392 2022-06-13 06:16 ./usr/bin/pxfqfilt 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root/root 191968 2022-06-13 06:16 ./usr/bin/pxrmt -rwxr-xr-x root/root 84448 2022-06-13 06:16 ./usr/bin/pxrr -rwxr-xr-x root/root 72160 2022-06-13 06:16 ./usr/bin/pxs2fa -rwxr-xr-x root/root 84448 2022-06-13 06:16 ./usr/bin/pxs2nex -rwxr-xr-x root/root 72160 2022-06-13 06:16 ./usr/bin/pxs2phy -rwxr-xr-x root/root 195048 2022-06-13 06:16 ./usr/bin/pxseqgen -rwxr-xr-x root/root 117224 2022-06-13 06:16 ./usr/bin/pxssort -rwxr-xr-x root/root 96736 2022-06-13 06:16 ./usr/bin/pxsstat -rwxr-xr-x root/root 240128 2022-06-13 06:16 ./usr/bin/pxstrec -rwxr-xr-x root/root 109032 2022-06-13 06:16 ./usr/bin/pxsw -rwxr-xr-x root/root 55776 2022-06-13 06:16 ./usr/bin/pxt2new -rwxr-xr-x root/root 55776 2022-06-13 06:16 ./usr/bin/pxt2nex -rwxr-xr-x root/root 68064 2022-06-13 06:16 ./usr/bin/pxtcol -rwxr-xr-x root/root 68064 2022-06-13 06:16 ./usr/bin/pxtcomb -rwxr-xr-x root/root 39400 2022-06-13 06:16 ./usr/bin/pxtgen -rwxr-xr-x root/root 100832 2022-06-13 06:16 ./usr/bin/pxtlate -rwxr-xr-x root/root 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+------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 410576 Build-Time: 106 Distribution: kinetic-proposed Host Architecture: amd64 Install-Time: 8 Job: phyx_1.3+ds-1build1.dsc Machine Architecture: amd64 Package: phyx Package-Time: 114 Source-Version: 1.3+ds-1build1 Space: 410576 Status: successful Version: 1.3+ds-1build1 -------------------------------------------------------------------------------- Finished at 2022-06-13T06:20:17Z Build needed 00:01:54, 410576k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23845385 Scanning for processes to kill in build PACKAGEBUILD-23845385