https://launchpad.net/ubuntu/+source/phyx/1.01+ds-2build1/+build/20274008 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-023 4.15.0-122-generic #124-Ubuntu SMP Thu Oct 15 13:09:19 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 10 Nov 14:20:55 ntpdate[1646]: adjust time server 10.211.37.1 offset 0.006095 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20274008 --image-type chroot /home/buildd/filecache-default/6663ab897c1b9684e4da3138ea2f806b3d40e7b1 Creating target for build PACKAGEBUILD-20274008 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20274008 Starting target for build PACKAGEBUILD-20274008 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20274008 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20274008 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20274008 Updating target for build PACKAGEBUILD-20274008 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [88.4 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [88.4 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main armhf Packages [1342 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe armhf Packages [12.7 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5332 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf Packages [207 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [90.7 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf Packages [1798 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [660 kB] Fetched 23.2 MB in 10s (2441 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.32 perl-modules-5.32 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common coreutils cpp-10 fakeroot g++-10 gcc-10 gcc-10-base grep libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdebconfclient0 libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgomp1 libidn2-0 libip4tc2 libmpc3 libncurses6 libncursesw6 libnpth0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 linux-libc-dev ncurses-base ncurses-bin perl perl-base readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata 68 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 214 MB of archives. After this operation, 632 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libcrypt-dev armhf 1:4.4.17-1ubuntu1 [113 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libcrypt1 armhf 1:4.4.17-1ubuntu1 [86.7 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libc6-dev armhf 2.32-0ubuntu4 [1581 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libc-dev-bin armhf 2.32-0ubuntu4 [29.6 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf linux-libc-dev armhf 5.8.0-26.27 [1135 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libtirpc-common all 1.2.6-3 [7444 B] Get:7 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libtirpc-dev armhf 1.2.6-3 [175 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libtirpc3 armhf 1.2.6-3 [66.1 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libcc1-0 armhf 10.2.0-16ubuntu1 [34.7 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf gcc-10-base armhf 10.2.0-16ubuntu1 [19.6 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libgcc-s1 armhf 10.2.0-16ubuntu1 [36.3 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libgomp1 armhf 10.2.0-16ubuntu1 [87.2 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libatomic1 armhf 10.2.0-16ubuntu1 [7240 B] Get:14 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libasan6 armhf 10.2.0-16ubuntu1 [328 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libubsan1 armhf 10.2.0-16ubuntu1 [122 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf g++-10 armhf 10.2.0-16ubuntu1 [63.0 MB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libstdc++-10-dev armhf 10.2.0-16ubuntu1 [1812 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libgcc-10-dev armhf 10.2.0-16ubuntu1 [716 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf gcc-10 armhf 10.2.0-16ubuntu1 [63.7 MB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf cpp-10 armhf 10.2.0-16ubuntu1 [57.0 MB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libstdc++6 armhf 10.2.0-16ubuntu1 [441 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libmpc3 armhf 1.2.0-1 [36.1 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libctf-nobfd0 armhf 2.35.1-2ubuntu1 [38.7 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libctf0 armhf 2.35.1-2ubuntu1 [37.6 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libbinutils armhf 2.35.1-2ubuntu1 [322 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf binutils-common armhf 2.35.1-2ubuntu1 [212 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf binutils armhf 2.35.1-2ubuntu1 [3368 B] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.35.1-2ubuntu1 [2060 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libc6 armhf 2.32-0ubuntu4 [2120 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main armhf base-files armhf 11ubuntu16 [60.2 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf bash armhf 5.1~rc2-1ubuntu1 [613 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf coreutils armhf 8.32-4ubuntu1 [1206 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf grep armhf 3.6-1 [143 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libncursesw6 armhf 6.2+20200918-1 [106 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libncurses6 armhf 6.2+20200918-1 [79.9 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libtinfo6 armhf 6.2+20200918-1 [74.2 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf ncurses-bin armhf 6.2+20200918-1 [165 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf perl-modules-5.32 all 5.32.0-4 [2753 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libperl5.32 armhf 5.32.0-4 [3338 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf perl armhf 5.32.0-4 [225 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf perl-base armhf 5.32.0-4 [1423 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libdebconfclient0 armhf 0.255ubuntu1 [5692 B] Get:43 http://ftpmaster.internal/ubuntu hirsute/main armhf base-passwd armhf 3.5.48 [46.0 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libc-bin armhf 2.32-0ubuntu4 [492 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf ncurses-base all 6.2+20200918-1 [18.7 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main armhf sysvinit-utils armhf 2.96-5ubuntu1 [19.2 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libgcrypt20 armhf 1.8.7-2ubuntu1 [364 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf systemd-timesyncd armhf 246.6-2ubuntu1 [27.8 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf systemd-sysv armhf 246.6-2ubuntu1 [10.3 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libapparmor1 armhf 3.0.0-0ubuntu3 [31.1 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main armhf libaudit-common all 1:2.8.5-3ubuntu2 [4092 B] Get:52 http://ftpmaster.internal/ubuntu hirsute/main armhf libaudit1 armhf 1:2.8.5-3ubuntu2 [36.2 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main armhf libcap2 armhf 1:2.44-1 [14.7 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main armhf libidn2-0 armhf 2.3.0-2 [49.7 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libip4tc2 armhf 1.8.5-3ubuntu3 [16.7 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main armhf libseccomp2 armhf 2.4.3-1ubuntu5 [32.6 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf systemd armhf 246.6-2ubuntu1 [3971 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libsystemd0 armhf 246.6-2ubuntu1 [247 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libudev1 armhf 246.6-2ubuntu1 [59.9 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main armhf libapt-pkg6.0 armhf 2.1.11 [773 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main armhf apt armhf 2.1.11 [1254 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main armhf libselinux1 armhf 3.1-2build1 [60.9 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main armhf libsemanage-common all 3.1-1build1 [10.1 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main armhf libsemanage1 armhf 3.1-1build1 [75.7 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf readline-common all 8.1~rc2-2 [54.1 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libreadline8 armhf 8.1~rc2-2 [115 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main armhf tzdata all 2020d-1ubuntu1 [293 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libfakeroot armhf 1.25.3-1 [23.2 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf fakeroot armhf 1.25.3-1 [60.9 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main armhf libnpth0 armhf 1.6-3 [6980 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 214 MB in 13s (16.8 MB/s) (Reading database ... 12723 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu1_armhf.deb ... Unpacking libcrypt-dev:armhf (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu1_armhf.deb ... Unpacking libcrypt1:armhf (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:armhf (1:4.4.17-1ubuntu1) ... (Reading database ... 12723 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.32-0ubuntu4_armhf.deb ... Unpacking libc6-dev:armhf (2.32-0ubuntu4) over (2.32-0ubuntu3) ... Preparing to unpack .../1-libc-dev-bin_2.32-0ubuntu4_armhf.deb ... Unpacking libc-dev-bin (2.32-0ubuntu4) over (2.32-0ubuntu3) ... Preparing to unpack .../2-linux-libc-dev_5.8.0-26.27_armhf.deb ... Unpacking linux-libc-dev:armhf (5.8.0-26.27) over (5.8.0-25.26) ... Preparing to unpack .../3-libtirpc-common_1.2.6-3_all.deb ... Unpacking libtirpc-common (1.2.6-3) over (1.2.6-1build1) ... Preparing to unpack .../4-libtirpc-dev_1.2.6-3_armhf.deb ... 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Changing home-directory of irc from /var/run/ircd to /run/ircd 1 changes have been made, rewriting files Writing passwd-file to /etc/passwd Writing shadow-file to /etc/shadow Writing group-file to /etc/group (Reading database ... 14642 files and directories currently installed.) Preparing to unpack .../libc-bin_2.32-0ubuntu4_armhf.deb ... Unpacking libc-bin (2.32-0ubuntu4) over (2.32-0ubuntu3) ... Setting up libc-bin (2.32-0ubuntu4) ... (Reading database ... 14642 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.2+20200918-1_all.deb ... Unpacking ncurses-base (6.2+20200918-1) over (6.2-1) ... Setting up ncurses-base (6.2+20200918-1) ... (Reading database ... 14642 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_2.96-5ubuntu1_armhf.deb ... Unpacking sysvinit-utils (2.96-5ubuntu1) over (2.96-3ubuntu1) ... Setting up sysvinit-utils (2.96-5ubuntu1) ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20274008 armhf hirsute-proposed -c chroot:build-PACKAGEBUILD-20274008 --arch=armhf --dist=hirsute-proposed --nolog phyx_1.01+ds-2build1.dsc Initiating build PACKAGEBUILD-20274008 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-122-generic #124-Ubuntu SMP Thu Oct 15 13:09:19 UTC 2020 armv7l sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-023.buildd +==============================================================================+ | phyx 1.01+ds-2build1 (armhf) Tue, 10 Nov 2020 14:22:44 +0000 | +==============================================================================+ Package: phyx Version: 1.01+ds-2build1 Source Version: 1.01+ds-2build1 Distribution: hirsute-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20274008/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- phyx_1.01+ds-2build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/phyx-rNCylp/phyx-1.01+ds' with '<>' I: NOTICE: Log filtering will replace 'build/phyx-rNCylp' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-8WximF/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-8WximF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8WximF/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-8WximF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8WximF/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-8WximF/apt_archive ./ Packages [434 B] Fetched 1740 B in 0s (45.2 kB/s) Reading package lists... Reading package lists... Install core 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: libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-8WximF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (37.2 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14642 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libatlas-cpp-0.6-dev, libarmadillo-dev Filtered Build-Depends: debhelper-compat (= 12), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libatlas-cpp-0.6-dev, libarmadillo-dev dpkg-deb: building package 'sbuild-build-depends-phyx-dummy' in '/<>/resolver-8WximF/apt_archive/sbuild-build-depends-phyx-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-phyx-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-8WximF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8WximF/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-8WximF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8WximF/apt_archive ./ Sources [538 B] Get:5 copy:/<>/resolver-8WximF/apt_archive ./ Packages [622 B] Fetched 2123 B in 0s (52.8 kB/s) Reading package lists... Reading package lists... Install phyx 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: libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarmadillo-dev libarmadillo10 libarpack2 libarpack2-dev libatlas-cpp-0.6-3 libatlas-cpp-0.6-dev libatlas-cpp-0.6-tools libblas-dev libblas3 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu67 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libmagic-mgc libmagic1 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtool libuchardet0 libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-minimal python3.8 python3.8-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libitpp-dev libatlas-cpp-doc liblapack-doc libhdf5-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 python3.8-venv python3.8-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarmadillo-dev libarmadillo10 libarpack2 libarpack2-dev libatlas-cpp-0.6-3 libatlas-cpp-0.6-dev libatlas-cpp-0.6-tools libblas-dev libblas3 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu67 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libmagic-mgc libmagic1 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtool libuchardet0 libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-minimal python3.8 python3.8-minimal sbuild-build-depends-phyx-dummy zlib1g-dev 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 30.4 MB of archives. After this operation, 121 MB of additional disk space will be used. 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hirsute/main armhf po-debconf all 1.0.21 [233 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main armhf debhelper all 13.2.1ubuntu1 [879 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/universe armhf hdf5-helpers armhf 1.10.6+repack-2 [13.7 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/universe armhf libaec0 armhf 1.0.4-1 [19.4 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main armhf libblas3 armhf 3.9.0-3ubuntu1 [97.8 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libgfortran5 armhf 10.2.0-16ubuntu1 [250 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main armhf liblapack3 armhf 3.9.0-3ubuntu1 [1637 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/universe armhf libarpack2 armhf 3.7.0-3 [79.9 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf libsuperlu5 armhf 5.2.2+dfsg1-2 [134 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf libarmadillo10 armhf 1:10.1.0+dfsg-2 [92.4 kB] Get:51 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[19.1 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf libarmadillo-dev armhf 1:10.1.0+dfsg-2 [382 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/universe armhf libatlas-cpp-0.6-3 armhf 0.6.4-3 [115 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main armhf pkg-config armhf 0.29.2-1ubuntu1 [43.4 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/universe armhf libatlas-cpp-0.6-tools armhf 0.6.4-3 [15.4 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/universe armhf libatlas-cpp-0.6-dev armhf 0.6.4-3 [34.4 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/universe armhf libnlopt0 armhf 2.6.1-8ubuntu3 [136 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/universe armhf libnlopt-dev armhf 2.6.1-8ubuntu3 [29.6 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/universe armhf libnlopt-cxx0 armhf 2.6.1-8ubuntu3 [155 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/universe armhf libnlopt-cxx-dev armhf 2.6.1-8ubuntu3 [11.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 30.4 MB in 2s (14.3 MB/s) Selecting previously unselected package libpython3.8-minimal:armhf. 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Setting up libblas3:armhf (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libsigsegv2:armhf (2.12-2build1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up libjpeg-turbo8:armhf (2.0.3-0ubuntu2) ... Setting up libgfortran5:armhf (10.2.0-16ubuntu1) ... Setting up libnlopt-cxx0:armhf (2.6.1-8ubuntu3) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu4) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libpython3.8-stdlib:armhf (3.8.6-1) ... Setting up libnlopt-dev:armhf (2.6.1-8ubuntu3) ... Setting up libatlas-cpp-0.6-tools (0.6.4-3) ... Setting up python3.8 (3.8.6-1) ... Setting up libelf1:armhf (0.182-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.2) ... Setting up libblas-dev:armhf (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up libsz2:armhf (1.0.4-1) ... Setting up libpython3-stdlib:armhf (3.8.6-1) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libjpeg-turbo8-dev:armhf (2.0.3-0ubuntu2) ... Setting up liblapack3:armhf (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libtool (2.4.6-14) ... Setting up libaec-dev:armhf (1.0.4-1) ... Setting up libarpack2:armhf (3.7.0-3) ... Setting up libsuperlu5:armhf (5.2.2+dfsg1-2) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.6-1) ... Setting up libnlopt-cxx-dev:armhf (2.6.1-8ubuntu3) ... Setting up liblapack-dev:armhf (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libcroco3:armhf (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up libatlas-cpp-0.6-dev:armhf (0.6.4-3) ... Setting up libhdf5-103-1:armhf (1.10.6+repack-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libhdf5-cpp-103-1:armhf (1.10.6+repack-2) ... Setting up libjpeg8-dev:armhf (8c-2ubuntu8) ... Setting up libsuperlu-dev:armhf (5.2.2+dfsg1-2) ... Setting up libhdf5-hl-100:armhf (1.10.6+repack-2) ... Setting up automake (1:1.16.2-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libarmadillo10 (1:10.1.0+dfsg-2) ... Setting up libarpack2-dev:armhf (3.7.0-3) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libjpeg-dev:armhf (8c-2ubuntu8) ... Setting up man-db (2.9.3-2) ... 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 intltool-debian (0.35.0+20060710.5) ... Setting up libhdf5-hl-cpp-100:armhf (1.10.6+repack-2) ... Setting up libhdf5-fortran-102:armhf (1.10.6+repack-2) ... Setting up libhdf5-hl-fortran-100:armhf (1.10.6+repack-2) ... Setting up po-debconf (1.0.21) ... Setting up libhdf5-dev (1.10.6+repack-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libarmadillo-dev (1:10.1.0+dfsg-2) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.2.1ubuntu1) ... Setting up sbuild-build-depends-phyx-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu4) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-122-generic arm64 (armv7l) Toolchain package versions: binutils_2.35.1-2ubuntu1 dpkg-dev_1.20.5ubuntu2 g++-10_10.2.0-16ubuntu1 gcc-10_10.2.0-16ubuntu1 libc6-dev_2.32-0ubuntu4 libstdc++-10-dev_10.2.0-16ubuntu1 libstdc++6_10.2.0-16ubuntu1 linux-libc-dev_5.8.0-26.27 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.11 autoconf_2.69-11.1 automake_1:1.16.2-4ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1~rc2-1ubuntu1 binutils_2.35.1-2ubuntu1 binutils-arm-linux-gnueabihf_2.35.1-2ubuntu1 binutils-common_2.35.1-2ubuntu1 bsdextrautils_2.36-3ubuntu1 bsdutils_1:2.36-3ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.32-4ubuntu1 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.0-16ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1ubuntu1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.5ubuntu2 dpkg-dev_1.20.5ubuntu2 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1 file_1:5.38-5 findutils_4.7.0-1ubuntu2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.0-16ubuntu1 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.0-16ubuntu1 gcc-10-base_10.2.0-16ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapparmor1_3.0.0-0ubuntu3 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libarmadillo-dev_1:10.1.0+dfsg-2 libarmadillo10_1:10.1.0+dfsg-2 libarpack2_3.7.0-3 libarpack2-dev_3.7.0-3 libasan6_10.2.0-16ubuntu1 libassuan0_2.5.3-7.1 libatlas-cpp-0.6-3_0.6.4-3 libatlas-cpp-0.6-dev_0.6.4-3 libatlas-cpp-0.6-tools_0.6.4-3 libatomic1_10.2.0-16ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3ubuntu2 libaudit1_1:2.8.5-3ubuntu2 libbinutils_2.35.1-2ubuntu1 libblas-dev_3.9.0-3ubuntu1 libblas3_3.9.0-3ubuntu1 libblkid1_2.36-3ubuntu1 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu4 libc-dev-bin_2.32-0ubuntu4 libc6_2.32-0ubuntu4 libc6-dev_2.32-0ubuntu4 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcc1-0_10.2.0-16ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.3-1ubuntu6 libctf-nobfd0_2.35.1-2ubuntu1 libctf0_2.35.1-2ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.255ubuntu1 libdebhelper-perl_13.2.1ubuntu1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.20.5ubuntu2 libelf1_0.182-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.3-1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-16ubuntu1 libgcc-s1_10.2.0-16ubuntu1 libgcrypt20_1.8.7-2ubuntu1 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.0-16ubuntu1 libglib2.0-0_2.66.2-1 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.6.15-4ubuntu2 libgomp1_10.2.0-16ubuntu1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-2 libip4tc2_1.8.5-3ubuntu3 libisl22_0.22.1-1 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_2.0.3-0ubuntu2 libjpeg-turbo8-dev_2.0.3-0ubuntu2 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c5_0.15-1 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-3_1.17-10 libkrb5support0_1.17-10 liblapack-dev_3.9.0-3ubuntu1 liblapack3_3.9.0-3ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3ubuntu1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnlopt-cxx-dev_2.6.1-8ubuntu3 libnlopt-cxx0_2.6.1-8ubuntu3 libnlopt-dev_2.6.1-8ubuntu3 libnlopt0_2.6.1-8ubuntu3 libnpth0_1.6-3 libnsl-dev_1.3.0-0ubuntu3 libnsl2_1.3.0-0ubuntu3 libnss-nis_3.1-0ubuntu4 libnss-nisplus_1.3-0ubuntu4 libp11-kit0_0.23.21-2build1 libpam-modules_1.3.1-5ubuntu6 libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libperl5.32_5.32.0-4 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpython3-stdlib_3.8.6-1 libpython3.8-minimal_3.8.6-1 libpython3.8-stdlib_3.8.6-1 libreadline8_8.1~rc2-2 libseccomp2_2.4.3-1ubuntu5 libselinux1_3.1-2build1 libsemanage-common_3.1-1build1 libsemanage1_3.1-1build1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.36-3ubuntu1 libsqlite3-0_3.33.0-1 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu4 libstdc++-10-dev_10.2.0-16ubuntu1 libstdc++6_10.2.0-16ubuntu1 libsub-override-perl_0.09-2 libsuperlu-dev_5.2.2+dfsg1-2 libsuperlu5_5.2.2+dfsg1-2 libsystemd0_246.6-2ubuntu1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-16ubuntu1 libuchardet0_0.0.7-1 libudev1_246.6-2ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36-3ubuntu1 libxml2_2.9.10+dfsg-6.2 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.0-26.27 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.36-3ubuntu1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 openssl_1.1.1f-1ubuntu4 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.32.0-4 perl-base_5.32.0-4 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-4 pinentry-curses_1.1.0-4build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 python3_3.8.6-1 python3-minimal_3.8.6-1 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 readline-common_8.1~rc2-2 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyx-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 systemd_246.6-2ubuntu1 systemd-sysv_246.6-2ubuntu1 systemd-timesyncd_246.6-2ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.30+dfsg-7 tzdata_2020d-1ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.36-3ubuntu1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Nov 10 11:03:02 2020 UTC gpgv: using RSA key EE240A052A231AD8925841D79B8EC849D5EF70ED gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phyx_1.01+ds-2build1.dsc dpkg-source: info: extracting phyx in /<>/phyx-1.01+ds dpkg-source: info: unpacking phyx_1.01+ds.orig.tar.xz dpkg-source: info: unpacking phyx_1.01+ds-2build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying link_lnlopt.patch dpkg-source: info: applying gcc10.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-20274008 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20274008 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20274008 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 1.01+ds-2build1 dpkg-buildpackage: info: source distribution hirsute dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/phyx-1.01+ds' rm -rf src/phyx.logfile if [ -r src/Makefile ]; then \ /usr/bin/make -C src distclean; \ fi make[1]: Leaving directory '/<>/phyx-1.01+ds' 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=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for fabs in -lm... yes checking for nlopt_version in -lnlopt... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking nlopt.h usability... yes checking nlopt.h presence... yes checking for nlopt.h... yes checking for library containing wrapper_sgesv_... -larmadillo checking fenv.h usability... yes checking fenv.h presence... yes checking for fenv.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for size_t... yes checking for stdlib.h... (cached) yes 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 -j4 make[1]: Entering directory '/<>/phyx-1.01+ds/src' g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "log.d" -o "log.o" "log.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "node.d" -o "node.o" "node.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tree.d" -o "tree.o" "tree.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tree_reader.d" -o "tree_reader.o" "tree_reader.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tree_utils.d" -o "tree_utils.o" "tree_utils.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "sequence.d" -o "sequence.o" "sequence.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_reader.d" -o "seq_reader.o" "seq_reader.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_utils.d" -o "seq_utils.o" "seq_utils.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_models.d" -o "seq_models.o" "seq_models.cpp" In file included from /usr/include/c++/10/vector:72, from tree_utils.cpp:9: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘bool postorder_ultrametricity_check(Node*, bool&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘double get_root_tip_var(Tree*)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘void set_node_heights(Node*)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘bool is_ultrametric_paths(Tree*)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "pairwise_alignment.d" -o "pairwise_alignment.o" "pairwise_alignment.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "superdouble.d" -o "superdouble.o" "superdouble.cpp" In file included from /usr/include/c++/10/vector:72, from pairwise_alignment.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_mrca.d" -o "main_mrca.o" "main_mrca.cpp" /usr/include/c++/10/bits/vector.tcc: In function ‘double nw(Sequence&, Sequence&, std::map >&, double, std::string&, std::string&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘double sw(Sequence&, Sequence&, std::map >&, double, std::string&, std::string&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_mrca_cut.d" -o "main_mrca_cut.o" "main_mrca_cut.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_mrca_name.d" -o "main_mrca_name.o" "main_mrca_name.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_consq.d" -o "main_consq.o" "main_consq.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "bd_sim.d" -o "bd_sim.o" "bd_sim.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_bd_sim.d" -o "main_bd_sim.o" "main_bd_sim.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tree_info.d" -o "tree_info.o" "tree_info.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_lstr.d" -o "main_lstr.o" "main_lstr.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_info.d" -o "seq_info.o" "seq_info.cpp" In file included from /usr/include/c++/10/map:60, from node.h:11, from tree.h:11, from bd_sim.h:8, from bd_sim.cpp:14: /usr/include/c++/10/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_lssq.d" -o "main_lssq.o" "main_lssq.cpp" In file included from /usr/include/c++/10/map:61, from node.h:11, from tree.h:11, from bd_sim.h:8, from bd_sim.cpp:14: /usr/include/c++/10/bits/stl_map.h: In member function ‘void BirthDeathSimulator::node_death(Node*)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function ‘void BirthDeathSimulator::node_birth(Node*)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function ‘Tree* BirthDeathSimulator::make_tree(bool)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "upgma.d" -o "upgma.o" "upgma.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_upgma.d" -o "main_upgma.o" "main_upgma.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "clsq.d" -o "clsq.o" "clsq.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_clsq.d" -o "main_clsq.o" "main_clsq.cpp" In file included from /usr/include/c++/10/map:60, from seq_info.cpp:2: /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "clean_tree.d" -o "clean_tree.o" "clean_tree.cpp" In file included from /usr/include/c++/10/vector:72, from upgma.cpp:11: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_cltr.d" -o "main_cltr.o" "main_cltr.cpp" In file included from /usr/include/c++/10/vector:67, from upgma.cpp:11: /usr/include/c++/10/bits/stl_vector.h: In function ‘void update_tree(std::string&, std::vector >&, std::map >&, int&, std::vector >&, int&, int&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_s2fa.d" -o "main_s2fa.o" "main_s2fa.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_s2phy.d" -o "main_s2phy.o" "main_s2phy.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_fqfilt.d" -o "main_fqfilt.o" "main_fqfilt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_revcomp.d" -o "main_revcomp.o" "main_revcomp.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "edlib.d" -o "edlib.o" "edlib.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_nw.d" -o "main_nw.o" "main_nw.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_sw.d" -o "main_sw.o" "main_sw.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_sample.d" -o "seq_sample.o" "seq_sample.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_boot.d" -o "main_boot.o" "main_boot.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "concat.d" -o "concat.o" "concat.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_concat.d" -o "main_concat.o" "main_concat.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "sstat.d" -o "sstat.o" "sstat.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_sstat.d" -o "main_sstat.o" "main_sstat.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "recode.d" -o "recode.o" "recode.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_recode.d" -o "main_recode.o" "main_recode.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_bp.d" -o "main_bp.o" "main_bp.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_t2new.d" -o "main_t2new.o" "main_t2new.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_t2nex.d" -o "main_t2nex.o" "main_t2nex.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rr.d" -o "main_rr.o" "main_rr.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d" -o "aa2cdn.o" "aa2cdn.cpp" In file included from /usr/include/c++/10/vector:72, from main_bp.cpp:5: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from main_bp.cpp:5: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from main_bp.cpp:5: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_aa2cdn.d" -o "main_aa2cdn.o" "main_aa2cdn.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tlate.d" -o "tlate.o" "tlate.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_tlate.d" -o "main_tlate.o" "main_tlate.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rms.d" -o "main_rms.o" "main_rms.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rmt.d" -o "main_rmt.o" "main_rmt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_trt.d" -o "main_trt.o" "main_trt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rmk.d" -o "main_rmk.o" "main_rmk.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "nj.d" -o "nj.o" "nj.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_nj.d" -o "main_nj.o" "main_nj.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "log_manip.d" -o "log_manip.o" "log_manip.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_log.d" -o "main_log.o" "main_log.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "vcf_reader.d" -o "vcf_reader.o" "vcf_reader.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_vcf2fa.d" -o "main_vcf2fa.o" "main_vcf2fa.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "relabel.d" -o "relabel.o" "relabel.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rlt.d" -o "main_rlt.o" "main_rlt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rls.d" -o "main_rls.o" "main_rls.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tscale.d" -o "tscale.o" "tscale.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_tscale.d" -o "main_tscale.o" "main_tscale.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "rate_model.d" -o "rate_model.o" "rate_model.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "state_reconstructor.d" -o "state_reconstructor.o" "state_reconstructor.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_nlopt.d" -o "optimize_state_reconstructor_nlopt.o" "optimize_state_reconstructor_nlopt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -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++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "branch_segment.d" -o "branch_segment.o" "branch_segment.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "cont_models.d" -o "cont_models.o" "cont_models.cpp" In file included from /usr/include/c++/10/vector:72, from rate_model.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const arma::Mat&}; _Tp = arma::Mat; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from rate_model.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void RateModel::set_n_qs(int)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from state_reconstructor.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BranchSegment&}; _Tp = BranchSegment; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from state_reconstructor.cpp:3: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void StateReconstructor::set_tree(Tree*)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from state_reconstructor.cpp:4: /usr/include/c++/10/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from state_reconstructor.cpp:4: /usr/include/c++/10/bits/stl_map.h: In member function ‘VectorNodeObject StateReconstructor::conditionals_periods(Node&)’: /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function ‘VectorNodeObject StateReconstructor::conditionals(Node&)’: /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function ‘void StateReconstructor::reverse(Node*)’: /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "seq_gen.d" -o "seq_gen.o" "seq_gen.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_strec.d" -o "main_strec.o" "main_strec.cpp" In file included from /usr/include/c++/10/map:60, from /usr/include/armadillo:42, from cont_models.cpp:5: /usr/include/c++/10/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from /usr/include/armadillo:42, from cont_models.cpp:5: /usr/include/c++/10/bits/stl_map.h: In function ‘double calc_bm_prune(Tree*, double)’: /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_seqgen.d" -o "main_seqgen.o" "main_seqgen.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_ssort.d" -o "main_ssort.o" "main_ssort.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_contrates.d" -o "main_contrates.o" "main_contrates.cpp" In file included from /usr/include/c++/10/vector:72, from main_strec.cpp:9: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from main_strec.cpp:9: /usr/include/c++/10/bits/stl_vector.h: In function ‘void parse_comma_list(std::string&, std::vector&) [with T = double]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from main_strec.cpp:9: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RateModel&}; _Tp = RateModel; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from main_strec.cpp:9: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RateModel; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "optimize_cont_models_nlopt.d" -o "optimize_cont_models_nlopt.o" "optimize_cont_models_nlopt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_tcol.d" -o "main_tcol.o" "main_tcol.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_tcomb.d" -o "main_tcomb.o" "main_tcomb.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "collapse_tree.d" -o "collapse_tree.o" "collapse_tree.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_colt.d" -o "main_colt.o" "main_colt.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "bd_fit.d" -o "bd_fit.o" "bd_fit.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_bd_fit.d" -o "main_bd_fit.o" "main_bd_fit.cpp" building pxmrca g++ -o "pxmrca" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_mrca.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxmrcacut g++ -o "pxmrcacut" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_mrca_cut.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxmrcaname g++ -o "pxmrcaname" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_mrca_name.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from bd_fit.cpp:6: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from bd_fit.cpp:6: /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 building pxconsq g++ -o "pxconsq" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_consq.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxbdsim g++ -o "pxbdsim" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize bd_sim.o main_bd_sim.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ building pxlstr g++ -o "pxlstr" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize tree_info.o main_lstr.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o bulding pxlssq g++ -o "pxlssq" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize seq_info.o main_lssq.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o /usr/include/c++/10/bits/stl_algo.h: In member function ‘void BDFit::fit_bd()’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ building pxupgma g++ -o "pxupgma" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize upgma.o main_upgma.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxclsq g++ -o "pxclsq" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize clsq.o main_clsq.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxcltr g++ -o "pxcltr" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize clean_tree.o main_cltr.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxs2fa g++ -o "pxs2fa" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2fa.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxs2phy g++ -o "pxs2phy" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2phy.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxs2nex g++ -o "pxs2nex" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2nex.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxfqfilt g++ -o "pxfqfilt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_fqfilt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrevcomp g++ -o "pxrevcomp" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_revcomp.o edlib.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxnw g++ -o "pxnw" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_nw.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxsw g++ -o "pxsw" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_sw.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxboot g++ -o "pxboot" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize seq_sample.o main_boot.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxcat g++ -o "pxcat" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize concat.o main_concat.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxsstat g++ -o "pxsstat" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize sstat.o main_sstat.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrecode g++ -o "pxrecode" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize recode.o main_recode.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxbp g++ -o "pxbp" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_bp.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxt2new g++ -o "pxt2new" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_t2new.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxt2nex g++ -o "pxt2nex" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_t2nex.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrr g++ -o "pxrr" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_rr.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxaa2cdn g++ -o "pxaa2cdn" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize aa2cdn.o main_aa2cdn.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtlate g++ -o "pxtlate" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize tlate.o main_tlate.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrms g++ -o "pxrms" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_rms.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrmt g++ -o "pxrmt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_rmt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtrt g++ -o "pxtrt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_trt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrmk g++ -o "pxrmk" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_rmk.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxnj g++ -o "pxnj" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize nj.o main_nj.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxlog g++ -o "pxlog" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize log_manip.o main_log.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxvcf2fa g++ -o "pxvcf2fa" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize vcf_reader.o main_vcf2fa.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrlt g++ -o "pxrlt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize relabel.o main_rlt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxrls g++ -o "pxrls" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize relabel.o main_rls.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtscale g++ -o "pxtscale" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize tscale.o main_tscale.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxstrec g++ -o "pxstrec" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_strec.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.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 -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt # -lgfortran building pxseqgen g++ -o "pxseqgen" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_seqgen.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.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 -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt building pxssort g++ -o "pxssort" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_ssort.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtcol g++ -o "pxtcol" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_tcol.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtcomb g++ -o "pxtcomb" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_tcomb.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxcolt g++ -o "pxcolt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize collapse_tree.o main_colt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxbdfit g++ -o "pxbdfit" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize bd_fit.o main_bd_fit.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo In file included from /usr/include/c++/10/vector:72, from /usr/include/nlopt.hpp:27, from optimize_cont_models_nlopt.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from /usr/include/nlopt.hpp:27, from optimize_cont_models_nlopt.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector optimize_single_rate_bm_bl(Tree*)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector optimize_single_rate_bm_nlopt(arma::rowvec&, arma::mat&, bool)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector optimize_single_rate_bm_ou_nlopt(arma::rowvec&, arma::mat&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ building pxcontrates g++ -o "pxcontrates" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -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 ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt make[1]: Leaving directory '/<>/phyx-1.01+ds/src' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/phyx-1.01+ds' cd src && python3 run_tests.py character: 0 character: 1 character: 2 ================= TESTING pxbdfit PASSED ================= TESTING pxboot PASSED ================= TESTING pxtscale PASSED ================= TESTING pxnw PASSED ================= TESTING pxs2phy PASSED ================= TESTING pxlog PASSED ================= TESTING pxrmk PASSED ================= TESTING pxmrca PASSED ================= TESTING pxconsq PASSED ================= TESTING pxtrt no test for pxtrt ================= TESTING pxrr PASSED ================= TESTING pxmrcaname PASSED ================= TESTING pxrevcomp PASSED ================= TESTING pxrmt PASSED ================= TESTING pxbdsim PASSED ================= TESTING pxaa2cdn PASSED ================= TESTING pxrms PASSED ================= TESTING pxsw PASSED ================= TESTING pxstrec PASSED ================= TESTING pxvcf2fa PASSED ================= TESTING pxclsq PASSED ================= TESTING pxfqfilt PASSED ================= TESTING pxt2nex PASSED ================= TESTING pxlssq PASSED ================= TESTING pxupgma PASSED ================= TESTING pxssort PASSED ================= TESTING pxrlt PASSED ================= TESTING pxbp PASSED ================= TESTING pxs2fa PASSED ================= TESTING pxtlate PASSED ================= TESTING pxcat PASSED ================= TESTING pxtcomb no test for pxtcomb ================= TESTING pxmrcacut PASSED ================= TESTING pxlstr PASSED ================= TESTING pxcltr no test for pxcltr ================= TESTING pxnj PASSED ================= TESTING pxrecode PASSED ================= TESTING pxtcol no test for pxtcol ================= TESTING pxt2new PASSED ================= TESTING pxs2nex PASSED ================= TESTING pxseqgen PASSED ================= TESTING pxcontrates PASSED ================= TESTING pxcolt PASSED ================= TESTING pxsstat PASSED ================= TESTING pxrls PASSED ================= PASSED TESTS: 41 FAILED TESTS: 0 make[1]: Leaving directory '/<>/phyx-1.01+ds' 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 '/<>/phyx-1.01+ds' mkdir -p /<>/phyx-1.01+ds/debian/phyx/usr/bin dh_auto_install -- prefix=/<>/phyx-1.01+ds/debian/phyx/usr cd src && make -j4 install DESTDIR=/<>/phyx-1.01\+ds/debian/phyx AM_UPDATE_INFO_DIR=no prefix=/<>/phyx-1.01\+ds/debian/phyx/usr make[2]: Entering directory '/<>/phyx-1.01+ds/src' install -m 0755 px* /<>/phyx-1.01+ds/debian/phyx/usr/bin make[2]: Leaving directory '/<>/phyx-1.01+ds/src' #echo "#!/usr/bin/python3" > /<>/phyx-1.01+ds/debian/phyx/usr/bin/Phyx_Gui #cat src/Phyx_Gui.py >> /<>/phyx-1.01+ds/debian/phyx/usr/bin/Phyx_Gui make[1]: Leaving directory '/<>/phyx-1.01+ds' 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_installinit -a -O--sourcedirectory=src dh_installsystemduser -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 '/<>/phyx-1.01+ds' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>/phyx-1.01+ds' dh_fixperms -a -O--sourcedirectory=src dh_missing -a -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxs2fa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxbp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxnw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxbdfit contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxlssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxconsq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtlate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtscale contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxboot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxsw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxt2nex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxaa2cdn contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxs2phy contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxs2nex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxstrec contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxfqfilt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxclsq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtcol contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxseqgen contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrecode contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtcomb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrlt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxbdsim contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxlog contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrevcomp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrmk contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxsstat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrmt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcolt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcontrates contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxmrcacut contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxtrt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxmrcaname contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxvcf2fa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrls contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxupgma contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxnj contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxcltr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxrms contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxt2new contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxlstr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxssort contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/phyx/usr/bin/pxmrca contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing phyx (in debian/phyx); do_strip: , oemstrip: pkgstriptranslations: processing phyx-dbgsym (in debian/.debhelper/phyx/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/phyx/DEBIAN/control, package phyx, directory debian/phyx pkgstripfiles: Running PNG optimization (using 4 cpus) for package phyx ... pkgstripfiles: No PNG files. dpkg-deb: building package 'phyx' in '../phyx_1.01+ds-2build1_armhf.deb'. pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com 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_1.01+ds-2build1_armhf.deb'. Renaming phyx-dbgsym_1.01+ds-2build1_armhf.deb to phyx-dbgsym_1.01+ds-2build1_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../phyx_1.01+ds-2build1_armhf.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 2020-11-10T14:28:57Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phyx_1.01+ds-2build1_armhf.changes: ----------------------------------- Format: 1.8 Date: Tue, 10 Nov 2020 11:03:00 +0000 Source: phyx Binary: phyx Architecture: armhf Version: 1.01+ds-2build1 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Dimitri John Ledkov Description: phyx - UNIX-style phylogenetic analyses on trees and sequences Changes: phyx (1.01+ds-2build1) hirsute; urgency=medium . * No change rebuild against new armadillo ABI. Checksums-Sha1: d8f21a6d4aeacf0b2984ef718b658a0ed086aef0 208820 phyx-dbgsym_1.01+ds-2build1_armhf.ddeb 3cbb0ea5c3916b32914085ede9a8123865003be5 7012 phyx_1.01+ds-2build1_armhf.buildinfo 1fa8f9c98832e15cfbefd209373296ad9baf6be1 1529516 phyx_1.01+ds-2build1_armhf.deb Checksums-Sha256: a5710bdc5c3d0ca950d775e3b4838ad803f6368b15cd0bd3325e40d81aae518e 208820 phyx-dbgsym_1.01+ds-2build1_armhf.ddeb 432416ab1cbcf236f6af186337a862a72a938ce44a66d5b0300d480eac1d49d1 7012 phyx_1.01+ds-2build1_armhf.buildinfo a293d5e477fb992446b0add4b54136cdd43e70adede8d35d773649182f96b21f 1529516 phyx_1.01+ds-2build1_armhf.deb Files: 5998b34170cd4387ede131749a2f16a2 208820 debug optional phyx-dbgsym_1.01+ds-2build1_armhf.ddeb 347e2d6c5d0516a799cd1e8f1d69162c 7012 science optional phyx_1.01+ds-2build1_armhf.buildinfo 4a64de0585957c87f449d4b6b23306a9 1529516 science optional phyx_1.01+ds-2build1_armhf.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phyx Binary: phyx phyx-dbgsym Architecture: armhf Version: 1.01+ds-2build1 Checksums-Md5: 5998b34170cd4387ede131749a2f16a2 208820 phyx-dbgsym_1.01+ds-2build1_armhf.ddeb 4a64de0585957c87f449d4b6b23306a9 1529516 phyx_1.01+ds-2build1_armhf.deb Checksums-Sha1: d8f21a6d4aeacf0b2984ef718b658a0ed086aef0 208820 phyx-dbgsym_1.01+ds-2build1_armhf.ddeb 1fa8f9c98832e15cfbefd209373296ad9baf6be1 1529516 phyx_1.01+ds-2build1_armhf.deb Checksums-Sha256: a5710bdc5c3d0ca950d775e3b4838ad803f6368b15cd0bd3325e40d81aae518e 208820 phyx-dbgsym_1.01+ds-2build1_armhf.ddeb a293d5e477fb992446b0add4b54136cdd43e70adede8d35d773649182f96b21f 1529516 phyx_1.01+ds-2build1_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Tue, 10 Nov 2020 14:28:56 +0000 Build-Path: /<>/phyx-1.01+ds Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.2-4ubuntu1), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.1~rc2-1ubuntu1), binutils (= 2.35.1-2ubuntu1), binutils-arm-linux-gnueabihf (= 2.35.1-2ubuntu1), binutils-common (= 2.35.1-2ubuntu1), bsdextrautils (= 2.36-3ubuntu1), bsdutils (= 1:2.36-3ubuntu1), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), coreutils (= 8.32-4ubuntu1), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.0-16ubuntu1), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2.1ubuntu1), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.5ubuntu2), dpkg-dev (= 1.20.5ubuntu2), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1ubuntu2), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.0-16ubuntu1), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.0-16ubuntu1), gcc-10-base (= 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2.36-3ubuntu1), libxml2 (= 2.9.10+dfsg-6.2), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.0-26.27), login (= 1:4.8.1-1ubuntu6), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), mime-support (= 3.64ubuntu1), ncurses-base (= 6.2+20200918-1), ncurses-bin (= 6.2+20200918-1), patch (= 2.7.6-6), perl (= 5.32.0-4), perl-base (= 5.32.0-4), perl-modules-5.32 (= 5.32.0-4), pkg-config (= 0.29.2-1ubuntu1), po-debconf (= 1.0.21), python3 (= 3.8.6-1), python3-minimal (= 3.8.6-1), python3.8 (= 3.8.6-1), python3.8-minimal (= 3.8.6-1), readline-common (= 8.1~rc2-2), rpcsvc-proto (= 1.4.2-0ubuntu4), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.13), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.30+dfsg-7), util-linux (= 2.36-3ubuntu1), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605006180" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phyx_1.01+ds-2build1_armhf.deb ------------------------------ new Debian package, version 2.0. size 1529516 bytes: control archive=3804 bytes. 1428 bytes, 23 lines control 8895 bytes, 120 lines md5sums Package: phyx Version: 1.01+ds-2build1 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 11164 Depends: libarmadillo10 (>= 1:10.1.0+dfsg), libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libnlopt0 (>= 2.6.1), libstdc++6 (>= 5.2), python3 Section: science Priority: optional Homepage: https://github.com/FePhyFoFum/phyx Description: UNIX-style phylogenetic analyses on trees and sequences phyx provides a convenient, lightweight and inclusive toolkit consisting of programs spanning the wide breadth of programs utilized by researchers performing phylogenomic analyses. Modeled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams. A result of this stream-centric approach is that, for most programs, only a single sequence or tree is in memory at any moment. Thus, large datasets can be processed with minimal memory requirements. phyx’s ever-growing complement of programs consists of over 35 programs focused on exploring, manipulating, analyzing and simulating phylogenetic objects (alignments, trees and MCMC logs). As with standard Unix command line tools, these programs can be piped (together with non-phyx tools), allowing the easy construction of efficient analytical pipelines. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2020-11-10 11:03 ./ drwxr-xr-x root/root 0 2020-11-10 11:03 ./usr/ drwxr-xr-x root/root 0 2020-11-10 11:03 ./usr/bin/ -rwxr-xr-x root/root 186008 2020-11-10 11:03 ./usr/bin/pxaa2cdn -rwxr-xr-x root/root 190104 2020-11-10 11:03 ./usr/bin/pxbdfit -rwxr-xr-x root/root 186008 2020-11-10 11:03 ./usr/bin/pxbdsim -rwxr-xr-x root/root 186008 2020-11-10 11:03 ./usr/bin/pxboot -rwxr-xr-x root/root 198296 2020-11-10 11:03 ./usr/bin/pxbp -rwxr-xr-x root/root 190104 2020-11-10 11:03 ./usr/bin/pxcat -rwxr-xr-x root/root 186008 2020-11-10 11:03 ./usr/bin/pxclsq -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxcltr -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxcolt -rwxr-xr-x root/root 177816 2020-11-10 11:03 ./usr/bin/pxconsq -rwxr-xr-x root/root 431776 2020-11-10 11:03 ./usr/bin/pxcontrates -rwxr-xr-x root/root 177816 2020-11-10 11:03 ./usr/bin/pxfqfilt -rwxr-xr-x root/root 198296 2020-11-10 11:03 ./usr/bin/pxlog -rwxr-xr-x root/root 202392 2020-11-10 11:03 ./usr/bin/pxlssq -rwxr-xr-x root/root 186008 2020-11-10 11:03 ./usr/bin/pxlstr -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxmrca -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxmrcacut -rwxr-xr-x root/root 186008 2020-11-10 11:03 ./usr/bin/pxmrcaname -rwxr-xr-x root/root 194200 2020-11-10 11:03 ./usr/bin/pxnj -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxnw -rwxr-xr-x root/root 252056 2020-11-10 11:03 ./usr/bin/pxrecode -rwxr-xr-x root/root 194200 2020-11-10 11:03 ./usr/bin/pxrevcomp -rwxr-xr-x root/root 194200 2020-11-10 11:03 ./usr/bin/pxrls -rwxr-xr-x root/root 190104 2020-11-10 11:03 ./usr/bin/pxrlt -rwxr-xr-x root/root 177816 2020-11-10 11:03 ./usr/bin/pxrmk -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxrms -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxrmt -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxrr -rwxr-xr-x root/root 177816 2020-11-10 11:03 ./usr/bin/pxs2fa -rwxr-xr-x root/root 177816 2020-11-10 11:03 ./usr/bin/pxs2nex -rwxr-xr-x root/root 177816 2020-11-10 11:03 ./usr/bin/pxs2phy -rwxr-xr-x root/root 407196 2020-11-10 11:03 ./usr/bin/pxseqgen -rwxr-xr-x root/root 226968 2020-11-10 11:03 ./usr/bin/pxssort -rwxr-xr-x root/root 186008 2020-11-10 11:03 ./usr/bin/pxsstat -rwxr-xr-x root/root 431776 2020-11-10 11:03 ./usr/bin/pxstrec -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxsw -rwxr-xr-x root/root 177816 2020-11-10 11:03 ./usr/bin/pxt2new -rwxr-xr-x root/root 177816 2020-11-10 11:03 ./usr/bin/pxt2nex -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxtcol -rwxr-xr-x root/root 186008 2020-11-10 11:03 ./usr/bin/pxtcomb -rwxr-xr-x root/root 190104 2020-11-10 11:03 ./usr/bin/pxtlate -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxtrt -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxtscale -rwxr-xr-x root/root 194200 2020-11-10 11:03 ./usr/bin/pxupgma -rwxr-xr-x root/root 181912 2020-11-10 11:03 ./usr/bin/pxvcf2fa drwxr-xr-x root/root 0 2020-11-10 11:03 ./usr/share/ drwxr-xr-x root/root 0 2020-11-10 11:03 ./usr/share/doc-base/ -rw-r--r-- root/root 1153 2020-04-17 19:56 ./usr/share/doc-base/phyx drwxr-xr-x root/root 0 2020-11-10 11:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-11-10 11:03 ./usr/share/doc/phyx/ -rw-r--r-- root/root 114860 2019-09-26 20:44 ./usr/share/doc/phyx/Phyxed_Manual.pdf -rw-r--r-- root/root 278 2020-04-17 19:56 ./usr/share/doc/phyx/README.test -rw-r--r-- root/root 923 2020-11-10 11:03 ./usr/share/doc/phyx/changelog.Debian.gz -rw-r--r-- root/root 982 2020-04-17 19:56 ./usr/share/doc/phyx/copyright drwxr-xr-x root/root 0 2020-11-10 11:03 ./usr/share/doc/phyx/examples/ drwxr-xr-x root/root 0 2019-09-26 20:44 ./usr/share/doc/phyx/examples/manuscript_example/ -rw-r--r-- root/root 18072 2019-09-26 20:44 ./usr/share/doc/phyx/examples/manuscript_example/test.fa -rw-r--r-- root/root 18072 2019-09-26 20:44 ./usr/share/doc/phyx/examples/manuscript_example/test0.fa -rw-r--r-- root/root 18072 2019-09-26 20:44 ./usr/share/doc/phyx/examples/manuscript_example/test1.fa -rw-r--r-- root/root 18072 2019-09-26 20:44 ./usr/share/doc/phyx/examples/manuscript_example/test2.fa -rw-r--r-- root/root 18072 2019-09-26 20:44 ./usr/share/doc/phyx/examples/manuscript_example/test3.fa -rw-r--r-- root/root 18072 2019-09-26 20:44 ./usr/share/doc/phyx/examples/manuscript_example/test4.fa drwxr-xr-x root/root 0 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxaa2cdn_example/ -rw-r--r-- root/root 21537 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxaa2cdn_example/AA_Alignment.fa -rw-r--r-- root/root 51027 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxaa2cdn_example/Unaligned_Nucleotide.fa drwxr-xr-x root/root 0 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbdfit_example/ -rw-r--r-- root/root 3059 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbdfit_example/bd.tre drwxr-xr-x root/root 0 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxboot_example/ -rw-r--r-- root/root 754 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxboot_example/Alignment -rw-r--r-- root/root 75 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxboot_example/parts drwxr-xr-x root/root 0 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbp_example/ -rw-r--r-- root/root 282 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbp_example/Tree.tre -rw-r--r-- root/root 142 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbp_example/bp_output drwxr-xr-x root/root 0 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbpseq_example/ -rw-r--r-- root/root 10051 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbpseq_example/Sequences.fa -rw-r--r-- root/root 0 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbpseq_example/out -rw-r--r-- root/root 282 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxbpseq_example/ultra_100.tre drwxr-xr-x root/root 0 2019-09-26 20:44 ./usr/share/doc/phyx/examples/pxcat_example/ -rw-r--r-- root/root 128 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Build-Time: 330 Distribution: hirsute-proposed Host Architecture: armhf Install-Time: 39 Job: phyx_1.01+ds-2build1.dsc Machine Architecture: arm64 Package: phyx Package-Time: 373 Source-Version: 1.01+ds-2build1 Space: n/a Status: successful Version: 1.01+ds-2build1 -------------------------------------------------------------------------------- Finished at 2020-11-10T14:28:57Z Build needed 00:06:13, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20274008 Scanning for processes to kill in build PACKAGEBUILD-20274008