https://launchpad.net/ubuntu/+source/phyx/1.3.1+ds-2build1/+build/26933471 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lgw01-002 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_234~642~ubuntu20.04.1 python3-lpbuildd_234~642~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 27 Oct 20:03:44 ntpdate[96431]: adjust time server 10.211.37.1 offset -0.002941 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-26933471 --image-type chroot /home/buildd/filecache-default/20a3246b7a16d5658607d7f37229fcda30a33651 Creating target for build PACKAGEBUILD-26933471 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-26933471 Starting target for build PACKAGEBUILD-26933471 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-26933471 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26933471 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-26933471 Updating target for build PACKAGEBUILD-26933471 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [213 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main riscv64 Packages [1338 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe riscv64 Packages [14.5 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [5966 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 Packages [166 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [76.1 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe riscv64 Packages [864 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [812 kB] Fetched 24.6 MB in 51s (488 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libunistring2 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libunistring5 The following packages will be upgraded: apt apt-utils base-passwd bash-completion debianutils diffutils grep libapt-pkg6.0 libc-bin libc-dev-bin libc6 libc6-dev libgnutls30 libidn2-0 liblzma5 libncursesw6 libpng16-16 libsqlite3-0 libssl3 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxxhash0 libzstd1 mawk ncurses-base ncurses-bin openssl optipng systemd systemd-dev systemd-sysv xz-utils 34 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 22.5 MB of archives. After this operation, 2046 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main riscv64 debianutils riscv64 5.14 [88.8 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 diffutils riscv64 1:3.10-1 [180 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main riscv64 grep riscv64 3.11-3 [167 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 ncurses-bin riscv64 6.4+20231016-1 [184 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libc6-dev riscv64 2.38-3ubuntu1 [3401 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libc-dev-bin riscv64 2.38-3ubuntu1 [19.2 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libc6 riscv64 2.38-3ubuntu1 [2742 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main riscv64 base-passwd riscv64 3.6.2 [52.1 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libc-bin riscv64 2.38-3ubuntu1 [601 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 ncurses-base all 6.4+20231016-1 [24.7 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 liblzma5 riscv64 5.4.4-0.1 [127 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libssl3 riscv64 3.0.10-1ubuntu2.1 [1712 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libzstd1 riscv64 1.5.5+dfsg2-2 [349 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 systemd-sysv riscv64 253.5-1ubuntu7 [11.5 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 systemd-dev all 253.5-1ubuntu7 [78.5 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 systemd riscv64 253.5-1ubuntu7 [3067 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsystemd-shared riscv64 253.5-1ubuntu7 [1903 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsystemd0 riscv64 253.5-1ubuntu7 [423 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libudev1 riscv64 253.5-1ubuntu7 [163 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libxxhash0 riscv64 0.8.2-2 [43.7 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libapt-pkg6.0 riscv64 2.7.6 [989 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 apt riscv64 2.7.6 [1335 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 apt-utils riscv64 2.7.6 [225 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main riscv64 libunistring5 riscv64 1.1-2 [544 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libidn2-0 riscv64 2.3.4-1build1 [99.3 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libgnutls30 riscv64 3.8.1-4ubuntu2 [1007 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libncursesw6 riscv64 6.4+20231016-1 [150 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libtinfo6 riscv64 6.4+20231016-1 [107 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 mawk riscv64 1.3.4.20230808-1 [125 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsqlite3-0 riscv64 3.43.2-1 [693 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 openssl riscv64 3.0.10-1ubuntu2.1 [1170 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main riscv64 bash-completion all 1:2.11-8 [180 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libpng16-16 riscv64 1.6.40-2 [189 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 xz-utils riscv64 5.4.4-0.1 [268 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 optipng riscv64 0.7.7-3 [86.9 kB] Preconfiguring packages ... Fetched 22.5 MB in 6s (3931 kB/s) (Reading database ... 13552 files and directories currently installed.) Preparing to unpack .../debianutils_5.14_riscv64.deb ... Unpacking debianutils (5.14) over (5.8-1) ... Setting up debianutils (5.14) ... (Reading database ... 13551 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-1_riscv64.deb ... Unpacking diffutils (1:3.10-1) over (1:3.8-4) ... Setting up diffutils (1:3.10-1) ... (Reading database ... 13551 files and directories currently installed.) Preparing to unpack .../grep_3.11-3_riscv64.deb ... Unpacking grep (3.11-3) over (3.11-2) ... Setting up grep (3.11-3) ... (Reading database ... 13551 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20231016-1_riscv64.deb ... Unpacking ncurses-bin (6.4+20231016-1) over (6.4+20230625-2) ... Setting up ncurses-bin (6.4+20231016-1) ... (Reading database ... 13551 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26933471 riscv64 noble-proposed -c chroot:build-PACKAGEBUILD-26933471 --arch=riscv64 --dist=noble-proposed --nolog phyx_1.3.1+ds-2build1.dsc Initiating build PACKAGEBUILD-26933471 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lgw01-002.buildd +==============================================================================+ | phyx 1.3.1+ds-2build1 (riscv64) Fri, 27 Oct 2023 20:09:35 +0000 | +==============================================================================+ Package: phyx Version: 1.3.1+ds-2build1 Source Version: 1.3.1+ds-2build1 Distribution: noble-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26933471/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/phyx-RMds6Z/resolver-cIQWdD' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- phyx_1.3.1+ds-2build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/phyx-RMds6Z/phyx-1.3.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/phyx-RMds6Z' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libarmadillo-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-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 [407 B] Get:5 copy:/<>/apt_archive ./ Packages [490 B] Fetched 1854 B in 1s (3390 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 packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 liblocale-gettext-perl libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev 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 libarmadillo12 libarpack2 libarpack2-dev libblas-dev libblas3 libbrotli1 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu72 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libldap2 libmagic-mgc libmagic1 libnghttp2-14 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsuperlu-dev libsuperlu6 libsz2 libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libitpp-dev liblapack-doc libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config 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 python3.11-venv python3.11-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev 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 libarmadillo12 libarpack2 libarpack2-dev libblas-dev libblas3 libbrotli1 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu72 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libldap2 libmagic-mgc libmagic1 libnghttp2-14 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsuperlu-dev libsuperlu6 libsz2 libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 58.6 MB of archives. After this operation, 300 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [700 B] Get:2 http://ftpmaster.internal/ubuntu noble/main riscv64 libpython3.11-minimal riscv64 3.11.6-3 [834 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main riscv64 libexpat1 riscv64 2.5.0-2 [78.2 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main riscv64 python3.11-minimal riscv64 3.11.6-3 [2147 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main riscv64 python3-minimal riscv64 3.11.4-5 [26.8 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main riscv64 media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main riscv64 libpython3.11-stdlib riscv64 3.11.6-3 [1906 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main riscv64 python3.11 riscv64 3.11.6-3 [579 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main riscv64 libpython3-stdlib riscv64 3.11.4-5 [9508 B] Get:10 http://ftpmaster.internal/ubuntu noble/main riscv64 python3 riscv64 3.11.4-5 [22.9 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main riscv64 libelf1 riscv64 0.189-4 [51.9 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main riscv64 libicu72 riscv64 72.1-3ubuntu3 [10.8 MB] Get:13 http://ftpmaster.internal/ubuntu noble/main riscv64 libxml2 riscv64 2.9.14+dfsg-1.3 [599 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libmagic-mgc riscv64 1:5.45-2 [307 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libmagic1 riscv64 1:5.45-2 [93.6 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 file riscv64 1:5.45-2 [21.7 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gettext-base riscv64 0.21-13build1 [41.6 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main riscv64 libuchardet0 riscv64 0.0.7-1build2 [78.9 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 groff-base riscv64 1.23.0-3 [1017 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libnghttp2-14 riscv64 1.57.0-1 [82.4 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main riscv64 libpipeline1 riscv64 1.5.7-1 [26.8 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libpsl5 riscv64 0.21.2-1build1 [57.2 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 man-db riscv64 2.12.0-1 [1214 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 m4 riscv64 1.4.19-4 [261 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main riscv64 autoconf all 2.71-3 [339 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main riscv64 autotools-dev all 20220109.1 [44.9 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main riscv64 automake all 1:1.16.5-1.3 [558 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 autopoint all 0.21-13build1 [422 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libdebhelper-perl all 13.11.7ubuntu1 [85.8 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main riscv64 libtool all 2.4.7-7 [166 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main riscv64 libsub-override-perl all 0.09-4 [8706 B] Get:34 http://ftpmaster.internal/ubuntu noble/main riscv64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main riscv64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:36 http://ftpmaster.internal/ubuntu noble/main riscv64 libdw1 riscv64 0.189-4 [234 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main riscv64 debugedit riscv64 1:5.0-5 [48.8 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main riscv64 dwz riscv64 0.15-1 [115 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gettext riscv64 0.21-13build1 [867 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main riscv64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 debhelper all 13.11.7ubuntu1 [940 kB] Get:43 http://ftpmaster.internal/ubuntu noble/universe riscv64 hdf5-helpers riscv64 1.10.8+repack1-1ubuntu1 [13.9 kB] Get:44 http://ftpmaster.internal/ubuntu noble/universe riscv64 libaec0 riscv64 1.0.6-1 [19.2 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main riscv64 libblas3 riscv64 3.11.0-2build1 [131 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main riscv64 libgfortran5 riscv64 13.2.0-4ubuntu3 [457 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main riscv64 liblapack3 riscv64 3.11.0-2build1 [2088 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/universe riscv64 libarpack2 riscv64 3.9.1-1 [92.9 kB] Get:49 http://ftpmaster.internal/ubuntu noble/universe riscv64 libsuperlu6 riscv64 6.0.0+dfsg1-3 [171 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/universe riscv64 libarmadillo12 riscv64 1:12.6.4+dfsg-1 [105 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main riscv64 libblas-dev riscv64 3.11.0-2build1 [295 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main riscv64 liblapack-dev riscv64 3.11.0-2build1 [13.0 MB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/universe riscv64 libarpack2-dev riscv64 3.9.1-1 [225 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main riscv64 libbrotli1 riscv64 1.0.9-2build8 [324 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main riscv64 libsasl2-modules-db riscv64 2.1.28+dfsg1-3 [21.5 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main riscv64 libsasl2-2 riscv64 2.1.28+dfsg1-3 [61.1 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main riscv64 libldap2 riscv64 2.6.6+dfsg-1~exp1ubuntu1 [201 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build4 [54.6 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main riscv64 libssh-4 riscv64 0.10.5-3ubuntu1 [195 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libcurl4 riscv64 8.2.1-1ubuntu3.1 [329 kB] Get:61 http://ftpmaster.internal/ubuntu noble/universe riscv64 libsz2 riscv64 1.0.6-1 [4734 B] Get:62 http://ftpmaster.internal/ubuntu noble/universe riscv64 libhdf5-103-1 riscv64 1.10.8+repack1-1ubuntu1 [1242 kB] Get:63 http://ftpmaster.internal/ubuntu noble/universe riscv64 libhdf5-fortran-102 riscv64 1.10.8+repack1-1ubuntu1 [73.3 kB] Get:64 http://ftpmaster.internal/ubuntu noble/universe riscv64 libhdf5-hl-100 riscv64 1.10.8+repack1-1ubuntu1 [49.8 kB] Get:65 http://ftpmaster.internal/ubuntu noble/universe riscv64 libhdf5-hl-fortran-100 riscv64 1.10.8+repack1-1ubuntu1 [26.7 kB] Get:66 http://ftpmaster.internal/ubuntu noble/universe riscv64 libhdf5-cpp-103-1 riscv64 1.10.8+repack1-1ubuntu1 [121 kB] Get:67 http://ftpmaster.internal/ubuntu noble/universe riscv64 libhdf5-hl-cpp-100 riscv64 1.10.8+repack1-1ubuntu1 [10.6 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main riscv64 zlib1g-dev riscv64 1:1.2.13.dfsg-1ubuntu5 [972 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main riscv64 libjpeg-turbo8 riscv64 2.1.5-2ubuntu1 [119 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main riscv64 libjpeg-turbo8-dev riscv64 2.1.5-2ubuntu1 [434 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main riscv64 libjpeg8 riscv64 8c-2ubuntu11 [2150 B] Get:72 http://ftpmaster.internal/ubuntu noble/main riscv64 libjpeg8-dev riscv64 8c-2ubuntu11 [1486 B] Get:73 http://ftpmaster.internal/ubuntu noble/main riscv64 libjpeg-dev riscv64 8c-2ubuntu11 [1484 B] Get:74 http://ftpmaster.internal/ubuntu noble/universe riscv64 libaec-dev riscv64 1.0.6-1 [44.2 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libcurl4-openssl-dev riscv64 8.2.1-1ubuntu3.1 [1049 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libssl-dev riscv64 3.0.10-1ubuntu2.1 [5120 kB] Get:77 http://ftpmaster.internal/ubuntu noble/universe riscv64 libhdf5-dev riscv64 1.10.8+repack1-1ubuntu1 [6172 kB] Get:78 http://ftpmaster.internal/ubuntu noble/universe riscv64 libsuperlu-dev riscv64 6.0.0+dfsg1-3 [20.7 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/universe riscv64 libarmadillo-dev riscv64 1:12.6.4+dfsg-1 [408 kB] Get:80 http://ftpmaster.internal/ubuntu noble/universe riscv64 libnlopt0 riscv64 2.7.1-5build1 [180 kB] Get:81 http://ftpmaster.internal/ubuntu noble/universe riscv64 libnlopt-dev riscv64 2.7.1-5build1 [43.9 kB] Get:82 http://ftpmaster.internal/ubuntu noble/universe riscv64 libnlopt-cxx0 riscv64 2.7.1-5build1 [209 kB] Get:83 http://ftpmaster.internal/ubuntu noble/universe riscv64 libnlopt-cxx-dev riscv64 2.7.1-5build1 [9962 B] Preconfiguring packages ... Fetched 58.6 MB in 14s (4115 kB/s) Selecting previously unselected package libpython3.11-minimal:riscv64. (Reading database ... 13547 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.6-3_riscv64.deb ... Unpacking libpython3.11-minimal:riscv64 (3.11.6-3) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.5.0-2_riscv64.deb ... Unpacking libexpat1:riscv64 (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.6-3_riscv64.deb ... Unpacking python3.11-minimal (3.11.6-3) ... Setting up libpython3.11-minimal:riscv64 (3.11.6-3) ... Setting up libexpat1:riscv64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.6-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 13861 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.4-5_riscv64.deb ... 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Setting up gettext-base (0.21-13build1) ... Setting up m4 (1.4.19-4) ... Setting up libnlopt0:riscv64 (2.7.1-5build1) ... Setting up file (1:5.45-2) ... Setting up libaec0:riscv64 (1.0.6-1) ... Setting up libsasl2-modules-db:riscv64 (2.1.28+dfsg1-3) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:riscv64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/riscv64-linux-gnu/libblas.so.3 (libblas.so.3-riscv64-linux-gnu) in auto mode Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libssl-dev:riscv64 (3.0.10-1ubuntu2.1) ... Setting up autopoint (0.21-13build1) ... Setting up libjpeg-turbo8:riscv64 (2.1.5-2ubuntu1) ... Setting up libsasl2-2:riscv64 (2.1.28+dfsg1-3) ... Setting up libssh-4:riscv64 (0.10.5-3ubuntu1) ... Setting up libgfortran5:riscv64 (13.2.0-4ubuntu3) ... Setting up autoconf (2.71-3) ... Setting up libnlopt-cxx0:riscv64 (2.7.1-5build1) ... Setting up zlib1g-dev:riscv64 (1:1.2.13.dfsg-1ubuntu5) ... Setting up libuchardet0:riscv64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libnlopt-dev:riscv64 (2.7.1-5build1) ... Setting up libelf1:riscv64 (0.189-4) ... Setting up libxml2:riscv64 (2.9.14+dfsg-1.3) ... Setting up libldap2:riscv64 (2.6.6+dfsg-1~exp1ubuntu1) ... Setting up libblas-dev:riscv64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so to provide /usr/lib/riscv64-linux-gnu/libblas.so (libblas.so-riscv64-linux-gnu) in auto mode Setting up libsz2:riscv64 (1.0.6-1) ... Setting up libpython3-stdlib:riscv64 (3.11.4-5) ... Setting up libjpeg8:riscv64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.6-3) ... Setting up libdw1:riscv64 (0.189-4) ... Setting up libjpeg-turbo8-dev:riscv64 (2.1.5-2ubuntu1) ... Setting up liblapack3:riscv64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/riscv64-linux-gnu/liblapack.so.3 (liblapack.so.3-riscv64-linux-gnu) in auto mode Setting up gettext (0.21-13build1) ... Setting up libtool (2.4.7-7) ... Setting up libaec-dev:riscv64 (1.0.6-1) ... Setting up libarpack2:riscv64 (3.9.1-1) ... Setting up python3 (3.11.4-5) ... Setting up libsuperlu6:riscv64 (6.0.0+dfsg1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libnlopt-cxx-dev:riscv64 (2.7.1-5build1) ... Setting up liblapack-dev:riscv64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so to provide /usr/lib/riscv64-linux-gnu/liblapack.so (liblapack.so-riscv64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:riscv64 (8.2.1-1ubuntu3.1) ... Setting up libjpeg8-dev:riscv64 (8c-2ubuntu11) ... Setting up libsuperlu-dev:riscv64 (6.0.0+dfsg1-3) ... Setting up libarmadillo12 (1:12.6.4+dfsg-1) ... Setting up libarpack2-dev:riscv64 (3.9.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:riscv64 (8c-2ubuntu11) ... Setting up man-db (2.12.0-1) ... 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 libcurl4-openssl-dev:riscv64 (8.2.1-1ubuntu3.1) ... Setting up libhdf5-103-1:riscv64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-cpp-103-1:riscv64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-hl-100:riscv64 (1.10.8+repack1-1ubuntu1) ... Setting up debhelper (13.11.7ubuntu1) ... Setting up libhdf5-hl-cpp-100:riscv64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-fortran-102:riscv64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-hl-fortran-100:riscv64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-dev (1.10.8+repack1-1ubuntu1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/riscv64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libarmadillo-dev (1:12.6.4+dfsg-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (253.5-1ubuntu7) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.41-5ubuntu1 dpkg-dev_1.22.0ubuntu1 g++-13_13.2.0-4ubuntu3 gcc-13_13.2.0-4ubuntu3 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-4ubuntu3 libstdc++6_13.2.0-4ubuntu3 linux-libc-dev_6.5.0-9.9 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.6 apt-utils_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13build1 autotools-dev_20220109.1 base-files_13ubuntu3 base-passwd_3.6.2 bash_5.2.15-2ubuntu1 bash-completion_1:2.11-8 binutils_2.41-5ubuntu1 binutils-common_2.41-5ubuntu1 binutils-riscv64-linux-gnu_2.41-5ubuntu1 bsdextrautils_2.39.1-4ubuntu2 bsdutils_1:2.39.1-4ubuntu2 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:13.2.0-1ubuntu1 cpp-13_13.2.0-4ubuntu3 dash_0.5.12-6ubuntu1 debconf_1.5.82 debconf-i18n_1.5.82 debhelper_13.11.7ubuntu1 debianutils_5.14 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.0ubuntu1 dpkg-dev_1.22.0ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1ubuntu1 g++-13_13.2.0-4ubuntu3 gcc_4:13.2.0-1ubuntu1 gcc-13_13.2.0-4ubuntu3 gcc-13-base_13.2.0-4ubuntu3 gettext_0.21-13build1 gettext-base_0.21-13build1 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 hdf5-helpers_1.10.8+repack1-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2ubuntu1 init-system-helpers_1.65.2ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-3ubuntu1 libacl1_2.3.1-3 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapparmor1_4.0.0~alpha2-0ubuntu5 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libarmadillo-dev_1:12.6.4+dfsg-1 libarmadillo12_1:12.6.4+dfsg-1 libarpack2_3.9.1-1 libarpack2-dev_3.9.1-1 libasan8_13.2.0-4ubuntu3 libassuan0_2.5.6-1 libatomic1_13.2.0-4ubuntu3 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-5ubuntu1 libblas-dev_3.11.0-2build1 libblas3_3.11.0-2build1 libblkid1_2.39.1-4ubuntu2 libbrotli1_1.0.9-2build8 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-3ubuntu1 libc-dev-bin_2.38-3ubuntu1 libc6_2.38-3ubuntu1 libc6-dev_2.38-3ubuntu1 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcc1-0_13.2.0-4ubuntu3 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libcryptsetup12_2:2.6.1-4ubuntu3 libctf-nobfd0_2.41-5ubuntu1 libctf0_2.41-5ubuntu1 libcurl4_8.2.1-1ubuntu3.1 libcurl4-openssl-dev_8.2.1-1ubuntu3.1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270ubuntu1 libdebhelper-perl_13.11.7ubuntu1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.0ubuntu1 libdw1_0.189-4 libelf1_0.189-4 libexpat1_2.5.0-2 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.32.1-1 libfdisk1_2.39.1-4ubuntu2 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-4ubuntu3 libgcc-s1_13.2.0-4ubuntu3 libgcrypt20_1.10.2-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.2.0-4ubuntu3 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.1-4ubuntu2 libgomp1_13.2.0-4ubuntu3 libgpg-error-l10n_1.47-2 libgpg-error0_1.47-2 libgpm2_1.20.7-10build1 libgssapi-krb5-2_1.20.1-3ubuntu1 libhdf5-103-1_1.10.8+repack1-1ubuntu1 libhdf5-cpp-103-1_1.10.8+repack1-1ubuntu1 libhdf5-dev_1.10.8+repack1-1ubuntu1 libhdf5-fortran-102_1.10.8+repack1-1ubuntu1 libhdf5-hl-100_1.10.8+repack1-1ubuntu1 libhdf5-hl-cpp-100_1.10.8+repack1-1ubuntu1 libhdf5-hl-fortran-100_1.10.8+repack1-1ubuntu1 libhogweed6_3.9.1-2 libicu72_72.1-3ubuntu3 libidn2-0_2.3.4-1build1 libip4tc2_1.8.9-2ubuntu2 libisl23_0.26-3 libjansson4_2.14-2 libjpeg-dev_8c-2ubuntu11 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg-turbo8-dev_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjpeg8-dev_8c-2ubuntu11 libjson-c5_0.17-1 libk5crypto3_1.20.1-3ubuntu1 libkeyutils1_1.6.3-2 libkmod2_30+20230519-1ubuntu3 libkrb5-3_1.20.1-3ubuntu1 libkrb5support0_1.20.1-3ubuntu1 liblapack-dev_3.11.0-2build1 liblapack3_3.11.0-2build1 libldap2_2.6.6+dfsg-1~exp1ubuntu1 liblocale-gettext-perl_1.07-6 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.1-4ubuntu2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231016-1 libnettle8_3.9.1-2 libnghttp2-14_1.57.0-1 libnlopt-cxx-dev_2.7.1-5build1 libnlopt-cxx0_2.7.1-5build1 libnlopt-dev_2.7.1-5build1 libnlopt0_2.7.1-5build1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libp11-kit0_0.25.0-4ubuntu1 libpam-modules_1.5.2-6ubuntu1 libpam-modules-bin_1.5.2-6ubuntu1 libpam-runtime_1.5.2-6ubuntu1 libpam0g_1.5.2-6ubuntu1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9ubuntu1 libpipeline1_1.5.7-1 libpng16-16_1.6.40-2 libproc2-0_2:4.0.3-1ubuntu1 libpsl5_0.21.2-1build1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.6-3 libpython3.11-stdlib_3.11.6-3 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1ubuntu3 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-5ubuntu1 libsmartcols1_2.39.1-4ubuntu2 libsqlite3-0_3.43.2-1 libss2_1.47.0-2ubuntu1 libssh-4_0.10.5-3ubuntu1 libssl-dev_3.0.10-1ubuntu2.1 libssl3_3.0.10-1ubuntu2.1 libstdc++-13-dev_13.2.0-4ubuntu3 libstdc++6_13.2.0-4ubuntu3 libsub-override-perl_0.09-4 libsuperlu-dev_6.0.0+dfsg1-3 libsuperlu6_6.0.0+dfsg1-3 libsystemd-shared_253.5-1ubuntu7 libsystemd0_253.5-1ubuntu7 libsz2_1.0.6-1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libuchardet0_0.0.7-1build2 libudev1_253.5-1ubuntu7 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.1-4ubuntu2 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.0-9.9 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_43 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-1 mawk_1.3.4.20230808-1 media-types_10.1.0 mount_2.39.1-4ubuntu2 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 openssl_3.0.10-1ubuntu2.1 optipng_0.7.7-3 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-9ubuntu1 perl-base_5.36.0-9ubuntu1 perl-modules-5.36_5.36.0-9ubuntu1 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.3-1ubuntu1 psmisc_23.6-1 python3_3.11.4-5 python3-minimal_3.11.4-5 python3.11_3.11.6-3 python3.11-minimal_3.11.6-3 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_253.5-1ubuntu7 systemd-dev_253.5-1ubuntu7 systemd-sysv_253.5-1ubuntu7 sysvinit-utils_3.07-1ubuntu1 tar_1.34+dfsg-1.2ubuntu1 tzdata_2023c-9ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.39.1-4ubuntu2 uuid-runtime_2.39.1-4ubuntu2 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-1ubuntu5 zlib1g-dev_1:1.2.13.dfsg-1ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phyx Binary: phyx Architecture: any Version: 1.3.1+ds-2build1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/FePhyFoFum/phyx Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/phyx Vcs-Git: https://salsa.debian.org/med-team/phyx.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libarmadillo-dev Package-List: phyx deb science optional arch=any Checksums-Sha1: b91fef57e035c34bf92fedc8d7dbc8cad0fbed0c 1191388 phyx_1.3.1+ds.orig.tar.xz 2e5ea8f3be96661fc492e5734657ea3f95e64572 10732 phyx_1.3.1+ds-2build1.debian.tar.xz Checksums-Sha256: ab788a470997954c3cec6a4b60d2d131ca3f129a3f8946f4b63041abeba35b53 1191388 phyx_1.3.1+ds.orig.tar.xz 3655b31ebf69f19870e71d43cf1d52b0d476688d54b9c1e6dec441482e1a5b75 10732 phyx_1.3.1+ds-2build1.debian.tar.xz Files: 874ffc6583f2de805514029b216d75a6 1191388 phyx_1.3.1+ds.orig.tar.xz 4fd9ff2a2e4ca776a5aee42f3c59dc3e 10732 phyx_1.3.1+ds-2build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEETQvhLw5HdtiqzpaW5mx3Wuv+bH0FAmU76j8ACgkQ5mx3Wuv+ bH3YKw/+ITonoAxxdY6g447k7OGcqd7beOFkadr64DPa6DgWQ6UcjSu0psDkmYpi p6yNzq5Qk9U4tnmWueANIBC7JV8yNJPYYNKCaiLhSAJkykbrtaU5+N9cHA346lBa /g7Kq+eGxHEfC8mvKu8yuvhkpWS+IdKT8B/r6J7pZD4VSp+E/6Ipxg6eaPxXv0LD n+NBr5OsiiSD3IkfOpicQuSS/sXWXNcl7bNFy4fIkLEGJCPxi6s93xsyYhCZ2n3g lcwfgxGah9J17Umgd4kWzMsJW67XVrWxSht0ayXYMzNYNehMxB0UiXllyBDuhYFn 2vxvVg3ZjKyP5QKcAVPqeDrSraIbaIfcRK9UgA57lIgP09Rr5mYtcnlWSu3Akbpr JQo8ApoMgNAAVskWzwrQh6WEQVO2t42dXLC570EQUswBLrCIIHOqDlgWtlOk3sJ1 nTorXYeFwBFUpXxOgiKk85tOqDZpOcNe0RqLDme8mh0ClOA0j7b4Vz6mN/cDP1KM l7V58Jie/UU1i4bc0y2ChO48grnFkg1WZOFB9U4yQEvdeHsTSZQWz5lH9yp6m2to 1x2iqOYdgW5ftgUacq2SlRJsIpnqVSFO+ldPxdokN/fAFcFUvXutXfZxZ3QJ3Lwx 7vl1CQJuv8AMUyMOPx/hb/ijKIaLs1j74VAO7ES6gHdfpEG460U= =TMOu -----END PGP SIGNATURE----- gpgv: Signature made Fri Oct 27 16:50:07 2023 UTC gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phyx_1.3.1+ds-2build1.dsc: no acceptable signature found dpkg-source: info: extracting phyx in /<> dpkg-source: info: unpacking phyx_1.3.1+ds.orig.tar.xz dpkg-source: info: unpacking phyx_1.3.1+ds-2build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying build-more-programs.patch dpkg-source: info: applying i386.patch dpkg-source: info: applying deoptimize.patch dpkg-source: info: applying whatis.patch dpkg-source: info: applying hardening.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 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-26933471 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26933471 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26933471 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 1.3.1+ds-2build1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 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-arch dh binary-arch --sourcedirectory=src dh_update_autotools_config -a -O--sourcedirectory=src dh_autoreconf -a -O--sourcedirectory=src dh_auto_configure -a -O--sourcedirectory=src cd src && ./configure --build=riscv64-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/riscv64-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... riscv64-unknown-linux-gnu checking host system type... riscv64-unknown-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 -a -O--sourcedirectory=src cd src && make -j8 make[1]: Entering directory '/<>/src' g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d" -o "aa2cdn.o" "aa2cdn.cpp" utils.cpp: In function ‘void v_mean_variance(std::vector&, double&, double&)’: utils.cpp:457:21: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 457 | std::bind2nd(std::minus(), mn)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438, from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from utils.cpp:1: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ utils.cpp: In function ‘double v_variance(std::vector&)’: utils.cpp:468:21: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 468 | std::bind2nd(std::minus(), meann)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ utils.cpp: In function ‘std::vector average_vectors_elementwise(std::vector&, std::vector&)’: utils.cpp:543:69: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = multiplies; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 543 | std::transform(res.begin(), res.end(), res.begin(), std::bind1st(std::multiplies(), 0.5)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP 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g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_cltr.d" -o "main_cltr.o" "main_cltr.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "collapse_tree.d" -o "collapse_tree.o" "collapse_tree.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions 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"polytomy.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_poly.d" -o "main_poly.o" "main_poly.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "recode.d" -o "recode.o" "recode.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_recode.d" -o "main_recode.o" "main_recode.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_revcomp.d" -o "main_revcomp.o" "main_revcomp.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "edlib.d" -o "edlib.o" "edlib.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "relabel.d" -o "relabel.o" "relabel.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rls.d" -o "main_rls.o" "main_rls.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "upgma.d" -o "upgma.o" "upgma.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_upgma.d" -o "main_upgma.o" "main_upgma.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rlt.d" -o "main_rlt.o" "main_rlt.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "nj.d" -o "nj.o" "nj.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_nj.d" -o "main_nj.o" "main_nj.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rmk.d" -o "main_rmk.o" "main_rmk.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rms.d" -o "main_rms.o" "main_rms.cpp" nj.cpp: In member function ‘void NJOI::CalcQ(const int&, std::vector >&, std::vector >&, std::vector >&)’: nj.cpp:69:25: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = multiplies; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 69 | std::bind1st(std::multiplies(), static_cast(NumbOfSequences - 2))); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438, from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from nj.cpp:1: /usr/include/c++/13/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rmt.d" -o "main_rmt.o" "main_rmt.cpp" g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_strec.d" -o "main_strec.o" "main_strec.cpp" building pxaa2cdn g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxaa2cdn" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize aa2cdn.o main_aa2cdn.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o building pxbdsim g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxbdsim" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize bd_sim.o main_bd_sim.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxaa2cdn.1.in > man/pxaa2cdn.1 building pxboot g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxboot" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize seq_sample.o main_boot.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxbdsim.1.in > man/pxbdsim.1 building pxbp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxbp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_bp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxboot.1.in > man/pxboot.1 building pxcat g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxcat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize concat.o main_cat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxbp.1.in > man/pxbp.1 building pxclsq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxclsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize clean_seq.o main_clsq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxcat.1.in > man/pxcat.1 building pxcltr g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxcltr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize clean_tree.o main_cltr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxcolt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxcolt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize collapse_tree.o main_colt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxcomp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize comp_test.o main_comp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxclsq.1.in > man/pxclsq.1 building pxconsq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxconsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_consq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxcltr.1.in > man/pxcltr.1 building pxfqfilt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxfqfilt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_fqfilt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxcolt.1.in > man/pxcolt.1 building pxlog g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxlog" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize log_manip.o main_log.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxcomp.1.in > man/pxcomp.1 bulding pxlssq g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxlssq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize seq_info.o main_lssq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxconsq.1.in > man/pxconsq.1 building pxlstr g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxlstr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tree_info.o main_lstr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxfqfilt.1.in > man/pxfqfilt.1 building pxmono g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxmono" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mono.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxlog.1.in > man/pxlog.1 building pxmrca g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxmrca" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxlssq.1.in > man/pxlssq.1 building pxmrcacut g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxmrcacut" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca_cut.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxlstr.1.in > man/pxlstr.1 building pxmrcaname g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxmrcaname" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_mrca_name.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxmono.1.in > man/pxmono.1 building pxnw g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxnw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_nw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxmrca.1.in > man/pxmrca.1 building pxpoly g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxpoly" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize polytomy.o main_poly.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxmrcacut.1.in > man/pxmrcacut.1 building pxrecode g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxrecode" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize recode.o main_recode.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxmrcaname.1.in > man/pxmrcaname.1 building pxrevcomp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxrevcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_revcomp.o edlib.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxnw.1.in > man/pxnw.1 building pxrls g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxrls" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize relabel.o main_rls.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxpoly.1.in > man/pxpoly.1 building pxupgma g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxupgma" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize upgma.o main_upgma.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrecode.1.in > man/pxrecode.1 building pxrlt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxrlt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize relabel.o main_rlt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrevcomp.1.in > man/pxrevcomp.1 building pxnj g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxnj" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize nj.o main_nj.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o building pxrmk g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxrmk" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rmk.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrls.1.in > man/pxrls.1 building pxrms g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxrms" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rms.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxupgma.1.in > man/pxupgma.1 building pxrmt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxrmt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rmt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxnj.1.in > man/pxnj.1 building pxrr g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxrr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_rr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxrlt.1.in > man/pxrlt.1 building pxs2fa g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxs2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrmk.1.in > man/pxrmk.1 building pxs2nex g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxs2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrmt.1.in > man/pxrmt.1 building pxs2phy g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxs2phy" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_s2phy.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxrms.1.in > man/pxrms.1 building pxseqgen g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -o "pxseqgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_seqgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxrr.1.in > man/pxrr.1 building pxssort g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxssort" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_ssort.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxs2fa.1.in > man/pxs2fa.1 building pxsstat g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxsstat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize sstat.o main_sstat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxs2nex.1.in > man/pxs2nex.1 building pxsw g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxsw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_sw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxs2phy.1.in > man/pxs2phy.1 building pxt2new g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxt2new" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_t2new.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxssort.1.in > man/pxssort.1 building pxt2nex g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxt2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_t2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxsstat.1.in > man/pxsstat.1 building pxtcol g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxtcol" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_tcol.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxsw.1.in > man/pxsw.1 building pxtcomb g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxtcomb" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_tcomb.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxt2new.1.in > man/pxt2new.1 building pxtgen g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxtgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tgen.o main_tgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxseqgen.1.in > man/pxseqgen.1 building pxtlate g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxtlate" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tlate.o main_tlate.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxt2nex.1.in > man/pxt2nex.1 building pxtrt g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxtrt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_trt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxtcol.1.in > man/pxtcol.1 building pxtscale g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxtscale" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize tscale.o main_tscale.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o cat man/pxtcomb.1.in > man/pxtcomb.1 building pxvcf2fa g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o "pxvcf2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize vcf_reader.o main_vcf2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o cat man/pxtgen.1.in > man/pxtgen.1 building pxbdfit g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -o "pxbdfit" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize bd_fit.o main_bd_fit.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxtlate.1.in > man/pxtlate.1 cat man/pxtrt.1.in > man/pxtrt.1 cat man/pxtscale.1.in > man/pxtscale.1 cat man/pxvcf2fa.1.in > man/pxvcf2fa.1 cat man/pxbdfit.1.in > man/pxbdfit.1 building pxcontrates g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -o "pxcontrates" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_contrates.o optimize_cont_models_nlopt.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo cat man/pxcontrates.1.in > man/pxcontrates.1 building pxstrec g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phyx-1.3.1+ds-2build1 -o "pxstrec" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize main_strec.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo # -lgfortran cat man/pxstrec.1.in > man/pxstrec.1 make[1]: Leaving directory '/<>/src' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=src dh_prep -a -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 -j8 install DESTDIR=/<>/phyx-1.3.1\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/<>/phyx-1.3.1\+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 -a -O--sourcedirectory=src dh_installchangelogs -a -O--sourcedirectory=src dh_installexamples -a -O--sourcedirectory=src dh_installman -a -O--sourcedirectory=src dh_installsystemduser -a -O--sourcedirectory=src dh_lintian -a -O--sourcedirectory=src dh_perl -a -O--sourcedirectory=src dh_link -a -O--sourcedirectory=src dh_strip_nondeterminism -a -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' dh_fixperms -a -O--sourcedirectory=src dh_missing -a -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src debugedit: debian/phyx/usr/bin/pxstrec: Unknown DWARF DW_FORM_0x1f20 142328d2ef45097412e7a377515f9226f4a09820 debugedit: debian/phyx/usr/bin/pxrmk: Unknown DWARF DW_FORM_0x1f21 dc1d93869d8418292e63a943ef19a92d0d8c4594 debugedit: debian/phyx/usr/bin/pxcltr: Unknown DWARF DW_FORM_0x1f20 bab18f061af1c22e822f88448540316e1b1cb402 debugedit: debian/phyx/usr/bin/pxlog: Unknown DWARF DW_FORM_0x1f21 3fe01ea359ac31d9eaf372f94b9a6b4fbba1bb64 debugedit: debian/phyx/usr/bin/pxt2new: Unknown DWARF DW_FORM_0x1f20 a9ee7a85f0e16395eff374fea061bfb00d755b63 debugedit: debian/phyx/usr/bin/pxtlate: Unknown DWARF DW_FORM_0x1f20 440af502bb36396188f4b29fc87c17a237cc9ee5 debugedit: debian/phyx/usr/bin/pxbdsim: Unknown DWARF DW_FORM_0x1f20 0de22b57516b97b6ec060052023e4ec3faf35753 debugedit: debian/phyx/usr/bin/pxvcf2fa: Unknown DWARF DW_FORM_0x1f21 582884d36b66b74f59b87671fb82f19822c9cd05 debugedit: debian/phyx/usr/bin/pxssort: Unknown DWARF DW_FORM_0x1f20 24ed5ca92185cb93d9e2195303a7f9a533b49eff debugedit: debian/phyx/usr/bin/pxcolt: Unknown DWARF DW_FORM_0x1f21 95d76b1f2fcc28a41fe65634db8db8647d38df1d debugedit: debian/phyx/usr/bin/pxupgma: Unknown DWARF DW_FORM_0x1f20 d022ab019e4732f42c781c478f908538f9c2fb0f debugedit: debian/phyx/usr/bin/pxs2fa: Unknown DWARF DW_FORM_0x1f20 6ec1c98f155beb7323df94a3528b271bb352fb1d debugedit: debian/phyx/usr/bin/pxaa2cdn: Unknown DWARF DW_FORM_0x1f20 5d0569c9ab7c72c0b462c1cbc4e1d20670ba2bdb debugedit: debian/phyx/usr/bin/pxlssq: Unknown DWARF DW_FORM_0x1f20 9b32d4c1bd51082ce9e9f88637095e78603431c2 debugedit: debian/phyx/usr/bin/pxbp: Unknown DWARF DW_FORM_0x1f20 e7d68961bc95bd4bcc8cc64b43676c9ef9e8391a debugedit: debian/phyx/usr/bin/pxs2phy: Unknown DWARF DW_FORM_0x1f20 03c7e3d285d70198f32dffc816bd39183486dc1d debugedit: debian/phyx/usr/bin/pxrevcomp: Unknown DWARF DW_FORM_0x1f20 8d1d5b473d11f01c15127ab768796a42143bcf70 debugedit: debian/phyx/usr/bin/pxtrt: Unknown DWARF DW_FORM_0x1f20 73063b57e533e817fc526c07190bb5f56c4d4f53 debugedit: debian/phyx/usr/bin/pxmrcaname: Unknown DWARF DW_FORM_0x1f20 b56095287c8884f7300b74ad3adcf2955290b40b debugedit: debian/phyx/usr/bin/pxbdfit: Unknown DWARF DW_FORM_0x1f20 8da187c735fa9aa61c44b7d634cd7d1dc74b7a59 debugedit: debian/phyx/usr/bin/pxsstat: Unknown DWARF DW_FORM_0x1f20 4aa1313aa157a5ff6b6167b57b3898e49562d9d4 debugedit: debian/phyx/usr/bin/pxnj: Unknown DWARF DW_FORM_0x1f20 60f676bff77d80016fe0e941efc0117f5e946fc6 debugedit: debian/phyx/usr/bin/pxnw: Unknown DWARF DW_FORM_0x1f21 028a6dd401656cce2ee4baab3f229882feea03c1 debugedit: debian/phyx/usr/bin/pxclsq: Unknown DWARF DW_FORM_0x1f20 ab19529788e5034abc5e619e355e52ad2fffdff4 debugedit: debian/phyx/usr/bin/pxrlt: Unknown DWARF DW_FORM_0x1f20 5d77bb52d710d1faa9b146887bbb4c4901b5dc8c debugedit: debian/phyx/usr/bin/pxrls: Unknown DWARF DW_FORM_0x1f20 35c0d7ee8a2c9a1665f97ceb1ee4496dd597ecc5 debugedit: debian/phyx/usr/bin/pxrms: Unknown DWARF DW_FORM_0x1f20 fd2a2ead3c63cb81e7bcc0aa1d4156e270094a6c debugedit: debian/phyx/usr/bin/pxs2nex: Unknown DWARF DW_FORM_0x1f20 ad0fef430665909ec43db9ea694e25b89f384b1b debugedit: debian/phyx/usr/bin/pxfqfilt: Unknown DWARF DW_FORM_0x1f21 9be4a35aeb90138d277215dedbefb6acfc40a3ef debugedit: debian/phyx/usr/bin/pxmono: Unknown DWARF DW_FORM_0x1f20 144d76ccf8d54087aa13540823586d432c062f1d debugedit: debian/phyx/usr/bin/pxpoly: Unknown DWARF DW_FORM_0x1f21 ea62cfc02963a1299e84d20434908fc688d1c3b4 debugedit: debian/phyx/usr/bin/pxboot: Unknown DWARF DW_FORM_0x1f20 670ed626bfd1d2e2b2dde5d64e5d989a3ef81ce4 debugedit: debian/phyx/usr/bin/pxmrca: Unknown DWARF DW_FORM_0x1f20 eba9b4692eb9778aaf5e80f60d9ff09747403619 debugedit: debian/phyx/usr/bin/pxseqgen: Unknown DWARF DW_FORM_0x1f20 e410b391b01f8d3ed3dc0285b4cbf236ad87559e debugedit: debian/phyx/usr/bin/pxtgen: Unknown DWARF DW_FORM_0x1f20 6bc8cdc897f3628c68c38d2c9549d78cc38a68d9 debugedit: debian/phyx/usr/bin/pxt2nex: Unknown DWARF DW_FORM_0x1f20 b47e369afaad5cf5720c515881301610c49da209 debugedit: debian/phyx/usr/bin/pxtcomb: Unknown DWARF DW_FORM_0x1f20 24d20230e34c9ac633672b356aaa3e593a7b3d98 debugedit: debian/phyx/usr/bin/pxconsq: Unknown DWARF DW_FORM_0x1f20 bae6222a7708c5fb91b6b2f17ff4d0eb8bc6cf25 debugedit: debian/phyx/usr/bin/pxcat: Unknown DWARF DW_FORM_0x1f20 935b8ff678d097754c2ce1a010a1acff28aaa558 debugedit: debian/phyx/usr/bin/pxcomp: Unknown DWARF DW_FORM_0x1f20 9977fbc92750da4e72c5f52d951225c125f0b404 debugedit: debian/phyx/usr/bin/pxrmt: Unknown DWARF DW_FORM_0x1f20 3c05c15dc82b9980be412ed706df47c951ac9dce debugedit: debian/phyx/usr/bin/pxcontrates: Unknown DWARF DW_FORM_0x1f20 d4414bf08a4a5acaf9b4ae7725352591cf004c4f debugedit: debian/phyx/usr/bin/pxtscale: Unknown DWARF DW_FORM_0x1f20 2725ccb467c9d094c1375fce10fa2673a1f9b440 debugedit: debian/phyx/usr/bin/pxsw: Unknown DWARF DW_FORM_0x1f20 f3319db6dbce294d5ce279734a805152e53ccb34 debugedit: debian/phyx/usr/bin/pxtcol: Unknown DWARF DW_FORM_0x1f20 a99fc48341a26a15dc7a668a414cfc3f34a6074c debugedit: debian/phyx/usr/bin/pxrecode: Unknown DWARF DW_FORM_0x1f20 f31d90c7da69356574049e737bf507899bf05fb4 debugedit: debian/phyx/usr/bin/pxlstr: Unknown DWARF DW_FORM_0x1f20 85216681bc0b1eb9d05af0af66419e59730743e1 debugedit: debian/phyx/usr/bin/pxmrcacut: Unknown DWARF DW_FORM_0x1f20 eb8a4ebb7af8559e5fc23a038c36bf62cf3fb1f7 debugedit: debian/phyx/usr/bin/pxrr: Unknown DWARF DW_FORM_0x1f20 dd6a04908955f12ac6ca3f2d131b41ce62f218ba dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dh_md5sums -a -O--sourcedirectory=src dh_builddeb -a -O--sourcedirectory=src INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing phyx (in debian/phyx); do_strip: , oemstrip: pkgstriptranslations: processing phyx-dbgsym (in debian/.debhelper/phyx/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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_1.3.1+ds-2build1_riscv64.deb'. pkgstripfiles: Running PNG optimization (using 8 cpus) for package phyx ... pkgstripfiles: No PNG files. dpkg-deb: building package 'phyx' in '../phyx_1.3.1+ds-2build1_riscv64.deb'. Renaming phyx-dbgsym_1.3.1+ds-2build1_riscv64.deb to phyx-dbgsym_1.3.1+ds-2build1_riscv64.ddeb dpkg-genbuildinfo --build=any -O../phyx_1.3.1+ds-2build1_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../phyx_1.3.1+ds-2build1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-10-27T20:48:50Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phyx_1.3.1+ds-2build1_riscv64.changes: -------------------------------------- Format: 1.8 Date: Fri, 27 Oct 2023 12:50:05 -0400 Source: phyx Binary: phyx Built-For-Profiles: noudeb Architecture: riscv64 Version: 1.3.1+ds-2build1 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Jeremy Bícha Description: phyx - UNIX-style phylogenetic analyses on trees and sequences Changes: phyx (1.3.1+ds-2build1) noble; urgency=medium . * Rebuild against latest armadillo Checksums-Sha1: dfba1637999df7a36464d1b9e7fc84bb8b98ff50 42397326 phyx-dbgsym_1.3.1+ds-2build1_riscv64.ddeb 157e3ea76b71f6c691b4d900842f1068b2b3322e 7577 phyx_1.3.1+ds-2build1_riscv64.buildinfo 5af42138d9e43e2f7162f3315810077904b906fa 2383618 phyx_1.3.1+ds-2build1_riscv64.deb Checksums-Sha256: 2daa098c3cf056834f61ff73719093897f8119f25bd9ebcf869505f71319013a 42397326 phyx-dbgsym_1.3.1+ds-2build1_riscv64.ddeb 90e9ab0dfdd98ec78e035d6b7dd761510b081499c5952b77b5deb91e5e14e5ed 7577 phyx_1.3.1+ds-2build1_riscv64.buildinfo 0c8e12a858f53ca222776cedead58e6a9a9f98523a2d8e4d9b76bdaa1662bfa3 2383618 phyx_1.3.1+ds-2build1_riscv64.deb Files: 3eb85ea5917ab598a644d082e1bfc1c1 42397326 debug optional 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+------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phyx_1.3.1+ds-2build1_riscv64.deb --------------------------------- new Debian package, version 2.0. size 2383618 bytes: control archive=5164 bytes. 1432 bytes, 23 lines control 12539 bytes, 176 lines md5sums Package: phyx Version: 1.3.1+ds-2build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 15650 Depends: libarmadillo12 (>= 1:12.6.4+dfsg), libc6 (>= 2.38), libgcc-s1 (>= 4.5), libgomp1 (>= 4.9), libnlopt0 (>= 2.6.1), libstdc++6 (>= 13.1), 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. drwxr-xr-x root/root 0 2023-10-27 16:50 ./ drwxr-xr-x root/root 0 2023-10-27 16:50 ./usr/ drwxr-xr-x root/root 0 2023-10-27 16:50 ./usr/bin/ -rwxr-xr-x root/root 287320 2023-10-27 16:50 ./usr/bin/pxaa2cdn -rwxr-xr-x root/root 250664 2023-10-27 16:50 ./usr/bin/pxbdfit -rwxr-xr-x root/root 250520 2023-10-27 16:50 ./usr/bin/pxbdsim -rwxr-xr-x root/root 258664 2023-10-27 16:50 ./usr/bin/pxboot -rwxr-xr-x root/root 262800 2023-10-27 16:50 ./usr/bin/pxbp -rwxr-xr-x root/root 258664 2023-10-27 16:50 ./usr/bin/pxcat -rwxr-xr-x root/root 262736 2023-10-27 16:50 ./usr/bin/pxclsq -rwxr-xr-x root/root 234104 2023-10-27 16:50 ./usr/bin/pxcltr -rwxr-xr-x root/root 234104 2023-10-27 16:50 ./usr/bin/pxcolt -rwxr-xr-x root/root 254560 2023-10-27 16:50 ./usr/bin/pxcomp -rwxr-xr-x root/root 246352 2023-10-27 16:50 ./usr/bin/pxconsq -rwxr-xr-x root/root 620032 2023-10-27 16:50 ./usr/bin/pxcontrates -rwxr-xr-x root/root 246352 2023-10-27 16:50 ./usr/bin/pxfqfilt -rwxr-xr-x root/root 266912 2023-10-27 16:50 ./usr/bin/pxlog -rwxr-xr-x root/root 275032 2023-10-27 16:50 ./usr/bin/pxlssq -rwxr-xr-x root/root 238192 2023-10-27 16:50 ./usr/bin/pxlstr -rwxr-xr-x root/root 238208 2023-10-27 16:50 ./usr/bin/pxmono -rwxr-xr-x root/root 238208 2023-10-27 16:50 ./usr/bin/pxmrca -rwxr-xr-x root/root 238208 2023-10-27 16:50 ./usr/bin/pxmrcacut -rwxr-xr-x root/root 242312 2023-10-27 16:50 ./usr/bin/pxmrcaname -rwxr-xr-x root/root 344744 2023-10-27 16:50 ./usr/bin/pxnj -rwxr-xr-x root/root 250496 2023-10-27 16:50 ./usr/bin/pxnw -rwxr-xr-x root/root 242312 2023-10-27 16:50 ./usr/bin/pxpoly -rwxr-xr-x root/root 262744 2023-10-27 16:50 ./usr/bin/pxrecode -rwxr-xr-x root/root 262792 2023-10-27 16:50 ./usr/bin/pxrevcomp -rwxr-xr-x root/root 348832 2023-10-27 16:50 ./usr/bin/pxrls -rwxr-xr-x root/root 344728 2023-10-27 16:50 ./usr/bin/pxrlt -rwxr-xr-x root/root 234096 2023-10-27 16:50 ./usr/bin/pxrmk -rwxr-xr-x root/root 258640 2023-10-27 16:50 ./usr/bin/pxrms -rwxr-xr-x root/root 238208 2023-10-27 16:50 ./usr/bin/pxrmt -rwxr-xr-x root/root 238208 2023-10-27 16:50 ./usr/bin/pxrr -rwxr-xr-x root/root 246352 2023-10-27 16:50 ./usr/bin/pxs2fa -rwxr-xr-x root/root 246352 2023-10-27 16:50 ./usr/bin/pxs2nex -rwxr-xr-x root/root 246352 2023-10-27 16:50 ./usr/bin/pxs2phy -rwxr-xr-x root/root 595472 2023-10-27 16:50 ./usr/bin/pxseqgen -rwxr-xr-x root/root 295504 2023-10-27 16:50 ./usr/bin/pxssort -rwxr-xr-x root/root 254544 2023-10-27 16:50 ./usr/bin/pxsstat -rwxr-xr-x root/root 624176 2023-10-27 16:50 ./usr/bin/pxstrec -rwxr-xr-x root/root 250496 2023-10-27 16:50 ./usr/bin/pxsw -rwxr-xr-x root/root 234112 2023-10-27 16:50 ./usr/bin/pxt2new -rwxr-xr-x root/root 234112 2023-10-27 16:50 ./usr/bin/pxt2nex -rwxr-xr-x root/root 238232 2023-10-27 16:50 ./usr/bin/pxtcol -rwxr-xr-x root/root 238200 2023-10-27 16:50 ./usr/bin/pxtcomb -rwxr-xr-x root/root 246376 2023-10-27 16:50 ./usr/bin/pxtgen -rwxr-xr-x root/root 270928 2023-10-27 16:50 ./usr/bin/pxtlate -rwxr-xr-x root/root 238208 2023-10-27 16:50 ./usr/bin/pxtrt -rwxr-xr-x root/root 234104 2023-10-27 16:50 ./usr/bin/pxtscale -rwxr-xr-x root/root 332440 2023-10-27 16:50 ./usr/bin/pxupgma -rwxr-xr-x root/root 250488 2023-10-27 16:50 ./usr/bin/pxvcf2fa drwxr-xr-x root/root 0 2023-10-27 16:50 ./usr/share/ drwxr-xr-x root/root 0 2023-10-27 16:50 ./usr/share/doc-base/ -rw-r--r-- root/root 1153 2023-08-15 08:45 ./usr/share/doc-base/phyx.phyx drwxr-xr-x root/root 0 2023-10-27 16:50 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-10-27 16:50 ./usr/share/doc/phyx/ -rw-r--r-- root/root 114860 2023-07-24 15:46 ./usr/share/doc/phyx/Phyxed_Manual.pdf -rw-r--r-- root/root 278 2023-08-15 08:45 ./usr/share/doc/phyx/README.test -rw-r--r-- root/root 1599 2023-10-27 16:50 ./usr/share/doc/phyx/changelog.Debian.gz -rw-r--r-- root/root 996 2023-08-15 08:45 ./usr/share/doc/phyx/copyright drwxr-xr-x root/root 0 2023-10-27 16:50 ./usr/share/doc/phyx/examples/ drwxr-xr-x root/root 0 2023-07-24 15:46 ./usr/share/doc/phyx/examples/manuscript_example/ -rw-r--r-- root/root 18072 2023-07-24 15:46 ./usr/share/doc/phyx/examples/manuscript_example/test.fa -rw-r--r-- root/root 18072 2023-07-24 15:46 ./usr/share/doc/phyx/examples/manuscript_example/test0.fa -rw-r--r-- root/root 18072 2023-07-24 15:46 ./usr/share/doc/phyx/examples/manuscript_example/test1.fa -rw-r--r-- root/root 18072 2023-07-24 15:46 ./usr/share/doc/phyx/examples/manuscript_example/test2.fa -rw-r--r-- root/root 18072 2023-07-24 15:46 ./usr/share/doc/phyx/examples/manuscript_example/test3.fa -rw-r--r-- root/root 18072 2023-07-24 15:46 ./usr/share/doc/phyx/examples/manuscript_example/test4.fa drwxr-xr-x root/root 0 2023-07-24 15:46 ./usr/share/doc/phyx/examples/pxaa2cdn_example/ -rw-r--r-- root/root 16338 2023-07-24 15:46 ./usr/share/doc/phyx/examples/pxaa2cdn_example/ND6_aa.fa 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 549184 Build-Time: 2048 Distribution: noble-proposed Host Architecture: riscv64 Install-Time: 275 Job: phyx_1.3.1+ds-2build1.dsc Machine Architecture: riscv64 Package: phyx Package-Time: 2355 Source-Version: 1.3.1+ds-2build1 Space: 549184 Status: successful Version: 1.3.1+ds-2build1 -------------------------------------------------------------------------------- Finished at 2023-10-27T20:48:50Z Build needed 00:39:15, 549184k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-26933471 Scanning for processes to kill in build PACKAGEBUILD-26933471 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-26933471 Stopping target for build PACKAGEBUILD-26933471 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-26933471 Removing build PACKAGEBUILD-26933471