https://launchpad.net/ubuntu/+source/libncl/2.1.21+git20190531.feceb81-2build1/+build/19106285 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-056 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 3 Apr 03:02:20 ntpdate[139914]: adjust time server 10.211.37.1 offset -0.000846 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19106285 --image-type chroot /home/buildd/filecache-default/88ad86cb2b525f1abddded96eadf8014548f7845 Creating target for build PACKAGEBUILD-19106285 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19106285 Starting target for build PACKAGEBUILD-19106285 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19106285 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-19106285 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19106285 Updating target for build PACKAGEBUILD-19106285 Ign:1 http://archive-team.internal/bootstrap/riscv64 focal InRelease Get:2 http://ftpmaster.internal/ubuntu focal InRelease [264 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal Release [760 B] Ign:4 http://archive-team.internal/bootstrap/riscv64 focal Release.gpg Get:5 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 Packages [1858 kB] Get:6 http://ftpmaster.internal/ubuntu focal-proposed InRelease [264 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 Packages [589 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main Translation-en [501 kB] Get:9 http://ftpmaster.internal/ubuntu focal/universe riscv64 Packages [4611 kB] Get:10 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5127 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 Packages [19.8 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [15.7 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 Packages [83.6 kB] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [98.1 kB] Fetched 13.4 MB in 21s (625 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: coreutils liblocale-gettext-perl libperl5.30 libtext-charwidth-perl libtext-iconv-perl perl-base 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6037 kB of archives. After this operation, 6144 B of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main riscv64 coreutils riscv64 8.30-3ubuntu2 [1158 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 perl-base riscv64 5.30.0-9build1 [1419 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 liblocale-gettext-perl riscv64 1.07-4 [16.5 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-charwidth-perl riscv64 0.04-10 [9460 B] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-iconv-perl riscv64 1.7-7 [13.2 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libperl5.30 riscv64 5.30.0-9build1 [3422 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6037 kB in 1s (5778 kB/s) (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_riscv64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu2) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../perl-base_5.30.0-9build1_riscv64.deb ... Unpacking perl-base (5.30.0-9build1) over (5.30.0-9build1) ... Setting up perl-base (5.30.0-9build1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-4) over (1.07-4) ... Preparing to unpack .../libtext-charwidth-perl_0.04-10_riscv64.deb ... Unpacking libtext-charwidth-perl (0.04-10) over (0.04-10) ... Preparing to unpack .../libtext-iconv-perl_1.7-7_riscv64.deb ... Unpacking libtext-iconv-perl (1.7-7) over (1.7-7) ... Preparing to unpack .../libperl5.30_5.30.0-9build1_riscv64.deb ... Unpacking libperl5.30:riscv64 (5.30.0-9build1) over (5.30.0-9build1) ... Setting up libtext-iconv-perl (1.7-7) ... Setting up libtext-charwidth-perl (0.04-10) ... Setting up libperl5.30:riscv64 (5.30.0-9build1) ... Setting up liblocale-gettext-perl (1.07-4) ... Processing triggers for libc-bin (2.31-0ubuntu6~riscv64.1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19106285 riscv64 focal -c chroot:build-PACKAGEBUILD-19106285 --arch=riscv64 --dist=focal --nolog libncl_2.1.21+git20190531.feceb81-2build1.dsc Initiating build PACKAGEBUILD-19106285 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-056 +=====================================================================================+ | libncl 2.1.21+git20190531.feceb81-2build1 (riscv64) Fri, 03 Apr 2020 03:04:13 +0000 | +=====================================================================================+ Package: libncl Version: 2.1.21+git20190531.feceb81-2build1 Source Version: 2.1.21+git20190531.feceb81-2build1 Distribution: focal Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19106285/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/libncl-WIcjYQ/resolver-60jgHu' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- libncl_2.1.21+git20190531.feceb81-2build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/libncl-WIcjYQ/libncl-2.1.21+git20190531.feceb81' with '<>' I: NOTICE: Log filtering will replace 'build/libncl-WIcjYQ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), d-shlibs, python3, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), d-shlibs, python3, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [382 B] Get:5 copy:/<>/apt_archive ./ Packages [466 B] Fetched 1805 B in 0s (4021 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support po-debconf python3 python3-minimal python3.8 python3.8-minimal tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff 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 bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support po-debconf python3 python3-minimal python3.8 python3.8-minimal sbuild-build-depends-main-dummy tzdata 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 21.4 MB of archives. After this operation, 85.7 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [888 B] Get:2 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libpython3.8-minimal riscv64 3.8.2-1ubuntu1 [698 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 libexpat1 riscv64 2.2.9-1build1 [68.8 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 python3-minimal riscv64 3.8.2-0ubuntu2 [23.6 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 mime-support all 3.64ubuntu1 [30.6 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libmpdec2 riscv64 2.4.2-3 [79.2 kB] Get:7 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libpython3-stdlib riscv64 3.8.2-0ubuntu2 [7072 B] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 python3 riscv64 3.8.2-0ubuntu2 [47.6 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main riscv64 libbsd0 riscv64 0.10.0-1 [42.0 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main riscv64 bsdmainutils riscv64 11.1.2ubuntu3 [176 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libuchardet0 riscv64 0.0.6-3build1 [64.9 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 libpipeline1 riscv64 1.5.2-2build1 [23.9 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 man-db riscv64 2.9.1-1 [1075 kB] Get:14 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 python3.8-minimal riscv64 3.8.2-1ubuntu1 [1447 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic-mgc riscv64 1:5.38-4 [218 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic1 riscv64 1:5.38-4 [70.5 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 file riscv64 1:5.38-4 [22.5 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 libelf1 riscv64 0.176-1.1build1 [41.8 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 tzdata all 2019c-3ubuntu1 [294 kB] Get:20 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libpython3.8-stdlib riscv64 3.8.2-1ubuntu1 [1558 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu66 riscv64 66.1-2ubuntu2 [8406 kB] Get:22 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 python3.8 riscv64 3.8.2-1ubuntu1 [364 kB] Get:23 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 groff-base riscv64 1.22.4-4build1 [815 kB] Get:24 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libglib2.0-0 riscv64 2.64.1-1 [1125 kB] Get:25 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 gettext-base riscv64 0.19.8.1-10build1 [47.4 kB] Get:26 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 dwz riscv64 0.13-5 [147 kB] Get:27 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libcroco3 riscv64 0.6.13-1 [71.0 kB] Get:28 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 gettext riscv64 0.19.8.1-10build1 [843 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main riscv64 libxml2 riscv64 2.9.10+dfsg-4build1 [558 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main riscv64 libsigsegv2 riscv64 2.12-2 [13.0 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main riscv64 m4 riscv64 1.4.18-4 [188 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main riscv64 autoconf all 2.69-11.1 [321 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main riscv64 autotools-dev all 20180224.1 [39.6 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main riscv64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main riscv64 autopoint all 0.19.8.1-10build1 [412 kB] Get:36 http://ftpmaster.internal/ubuntu focal/universe riscv64 d-shlibs all 0.89 [10.4 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main riscv64 libtool all 2.4.6-13 [161 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-autoreconf all 19 [16.1 kB] Get:39 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main riscv64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:42 http://ftpmaster.internal/ubuntu focal/main riscv64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:44 http://ftpmaster.internal/ubuntu focal/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main riscv64 po-debconf all 1.0.21 [233 kB] Get:46 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 debhelper all 12.10ubuntu1 [877 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.4 MB in 3s (6626 kB/s) Selecting previously unselected package libpython3.8-minimal:riscv64. (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.2-1ubuntu1_riscv64.deb ... Unpacking libpython3.8-minimal:riscv64 (3.8.2-1ubuntu1) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.2.9-1build1_riscv64.deb ... Unpacking libexpat1:riscv64 (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.2-1ubuntu1_riscv64.deb ... Unpacking python3.8-minimal (3.8.2-1ubuntu1) ... Setting up libpython3.8-minimal:riscv64 (3.8.2-1ubuntu1) ... Setting up libexpat1:riscv64 (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.2-1ubuntu1) ... Selecting previously unselected package python3-minimal. (Reading database ... 10109 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_riscv64.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... 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(Reading database ... 10511 files and directories currently installed.) Preparing to unpack .../00-python3_3.8.2-0ubuntu2_riscv64.deb ... Unpacking python3 (3.8.2-0ubuntu2) ... Selecting previously unselected package libbsd0:riscv64. Preparing to unpack .../01-libbsd0_0.10.0-1_riscv64.deb ... Unpacking libbsd0:riscv64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_11.1.2ubuntu3_riscv64.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../03-libuchardet0_0.0.6-3build1_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.6-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../04-groff-base_1.22.4-4build1_riscv64.deb ... Unpacking groff-base (1.22.4-4build1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../05-libpipeline1_1.5.2-2build1_riscv64.deb ... 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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../36-sbuild-build-depends-main-dummy_0.invalid.0_riscv64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:riscv64 (1.5.2-2build1) ... Setting up mime-support (3.64ubuntu1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-2) ... Setting up libglib2.0-0:riscv64 (2.64.1-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.10ubuntu1) ... Setting up libmagic1:riscv64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-4) ... Setting up tzdata (2019c-3ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Apr 3 03:06:31 UTC 2020. Universal Time is now: Fri Apr 3 03:06:31 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:riscv64 (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up d-shlibs (0.89) ... Setting up libuchardet0:riscv64 (0.0.6-3build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libmpdec2:riscv64 (2.4.2-3) ... Setting up libpython3.8-stdlib:riscv64 (3.8.2-1ubuntu1) ... Setting up python3.8 (3.8.2-1ubuntu1) ... Setting up libbsd0:riscv64 (0.10.0-1) ... Setting up libelf1:riscv64 (0.176-1.1build1) ... Setting up libpython3-stdlib:riscv64 (3.8.2-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libtool (2.4.6-13) ... Setting up libicu66:riscv64 (66.1-2ubuntu2) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.2-0ubuntu2) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4build1) ... Setting up libxml2:riscv64 (2.9.10+dfsg-4build1) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.10ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu6~riscv64.1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 (riscv64) Toolchain package versions: binutils_2.34-5ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-8ubuntu1 gcc-9_9.3.0-8ubuntu1 libc6-dev_2.31-0ubuntu6~riscv64.1 libstdc++-9-dev_9.3.0-8ubuntu1 libstdc++6_10-20200324-1ubuntu1 linux-libc-dev_5.4.0-21.25 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.1 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu4 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-5ubuntu1 binutils-common_2.34-5ubuntu1 binutils-riscv64-linux-gnu_2.34-5ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu8 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-8ubuntu1 d-shlibs_0.89 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 file_1:5.38-4 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-8ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200324-1ubuntu1 gcc-8-base_8.4.0-3ubuntu1 gcc-9_9.3.0-8ubuntu1 gcc-9-base_9.3.0-8ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 hostname_3.23 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libgcc-s1_10-20200324-1ubuntu1 libgcc1_1:10-20200324-1ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.11.1-2ubuntu2 libgomp1_10-20200324-1ubuntu1 libgpg-error0_1.37-1 libgpm2_1.20.7-5 libhogweed5_3.5.1+really3.5.1-2 libicu66_66.1-2ubuntu2 libidn2-0_2.2.0-2 libisl22_0.22.1-1 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1ubuntu8 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncursesw6_6.2-0ubuntu2 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.0-9build1 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8-minimal_3.8.2-1ubuntu1 libpython3.8-stdlib_3.8.2-1ubuntu1 libreadline8_8.0-4 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu8 libsqlite3-0_3.31.1-4 libss2_1.45.5-2ubuntu1 libssl1.1_1.1.1d-2ubuntu6 libstdc++-9-dev_9.3.0-8ubuntu1 libstdc++6_10-20200324-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244.3-1ubuntu1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-0ubuntu2 libtool_2.4.6-13 libuchardet0_0.0.6-3build1 libudev1_244.3-1ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu8 libxml2_2.9.10+dfsg-4build1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-21.25 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu3 logsave_1.45.5-2ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu8 ncurses-base_6.2-0ubuntu2 ncurses-bin_6.2-0ubuntu2 openssl_1.1.1d-2ubuntu6 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu3 patch_2.7.6-6 perl_5.30.0-9build1 perl-base_5.30.0-9build1 perl-modules-5.30_5.30.0-9build1 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 python3_3.8.2-0ubuntu2 python3-minimal_3.8.2-0ubuntu2 python3.8_3.8.2-1ubuntu1 python3.8-minimal_3.8.2-1ubuntu1 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1ubuntu1 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 util-linux_2.34-0.1ubuntu8 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libncl Binary: ncl-tools, libncl2, libncl-dev Architecture: any Version: 2.1.21+git20190531.feceb81-2build1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/mtholder/ncl Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/libncl Vcs-Git: https://salsa.debian.org/med-team/libncl.git Build-Depends: debhelper-compat (= 12), d-shlibs, python3 Package-List: libncl-dev deb libdevel optional arch=any libncl2 deb libs optional arch=any ncl-tools deb science optional arch=any Checksums-Sha1: 79497c4e753de381268b623d538641578bd6dc56 543968 libncl_2.1.21+git20190531.feceb81.orig.tar.xz 7991580bb81e62394e715a7327a00d80f848a284 20000 libncl_2.1.21+git20190531.feceb81-2build1.debian.tar.xz Checksums-Sha256: 6f55b5637e30781d6e1d557bdbc152d999c2f4f4d86b91a2238c3855791a648d 543968 libncl_2.1.21+git20190531.feceb81.orig.tar.xz f36a6cb4ae811273479874b8de25686ffea9c0668a5c25d291bb636331b67dbc 20000 libncl_2.1.21+git20190531.feceb81-2build1.debian.tar.xz Files: 6247cc411c82b6a76ebb6e9b4329301e 543968 libncl_2.1.21+git20190531.feceb81.orig.tar.xz 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UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libncl_2.1.21+git20190531.feceb81-2build1.dsc dpkg-source: info: extracting libncl in /<> dpkg-source: info: unpacking libncl_2.1.21+git20190531.feceb81.orig.tar.xz dpkg-source: info: unpacking libncl_2.1.21+git20190531.feceb81-2build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_rpath_issue.patch dpkg-source: info: applying set_soname_version.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.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-19106285 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19106285 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19106285 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20190531.feceb81-2build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 fakeroot debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean find . -name ".roundTripNCL*" -delete make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'. libtoolize: copying file 'config/libtool.m4' libtoolize: copying file 'config/ltoptions.m4' libtoolize: copying file 'config/ltsugar.m4' libtoolize: copying file 'config/ltversion.m4' libtoolize: copying file 'config/lt~obsolete.m4' configure.ac:28: installing 'config/compile' configure.ac:21: installing 'config/missing' example/basiccmdline/Makefile.am: installing 'config/depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --with-constfuncs=yes ./configure --build=riscv64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/riscv64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-constfuncs=yes configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '2001' is supported by ustar format... yes checking whether GID '2501' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... riscv64-unknown-linux-gnu checking host system type... riscv64-unknown-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert riscv64-unknown-linux-gnu file names to riscv64-unknown-linux-gnu format... func_convert_file_noop checking how to convert riscv64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C++ compiler works... yes checking for ANSI C header files... (cached) yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for inline... inline checking whether struct tm is in sys/time.h or time.h... time.h checking whether time.h and sys/time.h may both be included... yes checking for sys/time.h... yes checking for unistd.h... 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-fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o patristic.o patristic.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/<>/example/patristic' Making all in phylobaseinterface make[4]: Entering directory '/<>/example/phylobaseinterface' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLInterface.o NCLInterface.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/<>/example/phylobaseinterface' Making all in polytomy-count make[4]: Entering directory '/<>/example/polytomy-count' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o polytomycount-polytomy_count.o `test -f 'polytomy_count.cpp' || echo './'`polytomy_count.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/<>/example/polytomy-count' Making all in splitsinfile make[4]: Entering directory '/<>/example/splitsinfile' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStosplits-splitsinfile.o `test -f 'splitsinfile.cpp' || echo './'`splitsinfile.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStosplits-splitsstructs.o `test -f 'splitsstructs.cpp' || echo './'`splitsstructs.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsinfile.o splitsinfile.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/<>/example/splitsinfile' Making all in subsetter make[4]: Entering directory '/<>/example/subsetter' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSsubsetter-subsetter.o `test -f 'subsetter.cpp' || echo './'`subsetter.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/<>/example/subsetter' Making all in translate make[4]: Entering directory '/<>/example/translate' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStranslate-translateNuc.o `test -f 'translateNuc.cpp' || echo './'`translateNuc.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/<>/example/translate' make[4]: Entering directory '/<>/example' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/<>/example' make[3]: Leaving directory '/<>/example' Making all in test make[3]: Entering directory '/<>/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/test' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/<>' Making check in ncl make[2]: Entering directory '/<>/ncl' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/ncl' Making check in example make[2]: Entering directory '/<>/example' Making check in basiccmdline make[3]: Entering directory '/<>/example/basiccmdline' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/basiccmdline' Making check in check-taxo-nodes make[3]: Entering directory '/<>/example/check-taxo-nodes' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/check-taxo-nodes' Making check in compressor make[3]: Entering directory '/<>/example/compressor' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/compressor' Making check in find-unsupported-edges make[3]: Entering directory '/<>/example/find-unsupported-edges' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/find-unsupported-edges' Making check in gapcode make[3]: Entering directory '/<>/example/gapcode' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/gapcode' Making check in nclsimplest make[3]: Entering directory '/<>/example/nclsimplest' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/nclsimplest' Making check in ncltest make[3]: Entering directory '/<>/example/ncltest' make check-local make[4]: Entering directory '/<>/example/ncltest' /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/ncltest/ncltest ../../test/OldValidIn ../../test/OldValidOut [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing implied block: TAXA storing read block: DATA "/<>/example/ncltest/ncltest" "-s2" "/<>/test/OldValidIn/m.nex" ../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") ../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /<>/example/ncltest/ncltest succeeded for /<>/test/OldValidIn/m.nex "/<>/example/ncltest/ncltest" "-s2" "/<>/test/OldValidOut/m.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/ncltest/ncltest succeeded for /<>/test/OldValidOut/m.nex make[4]: Leaving directory '/<>/example/ncltest' make[3]: Leaving directory '/<>/example/ncltest' Making check in normalizer make[3]: Entering directory '/<>/example/normalizer' make check-local make[4]: Entering directory '/<>/example/normalizer' /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/characters.nex ../../test/data [Reading /<>/data/characters.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS [Reading /<>/test/data/characters.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/data/characters.nex" ../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") ../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/data/characters.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/data/characters.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/data/characters.nex /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/sample.tre ../../test/data [Reading /<>/data/sample.tre ] Executing storing read block: PAUP storing read block: TAXA storing read block: TREES [Reading /<>/test/data/sample.tre ] Executing storing read block: PAUP storing read block: TAXA storing read block: TREES "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/data/sample.tre" ../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") ../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/data/sample.tre "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/data/sample.tre" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/data/sample.tre /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut [Reading /<>/test/NTSValidIn/bglobin.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES [Reading /<>/test/NTSValidOut/bglobin.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES [Reading /<>/test/NTSValidIn/anolis.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES [Reading /<>/test/NTSValidOut/anolis.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES [Reading /<>/test/NTSValidIn/characters.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS [Reading /<>/test/NTSValidOut/characters.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS [Reading /<>/test/NTSValidIn/basic-bush-dos.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidOut/basic-bush-dos.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidIn/nhxtree.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: CODONS Warning: An * is ignored in a CHARSET command at line 67, column (approximately) 46 (file position 1014) Warning: An * is ignored in a CHARSET command at line 68, column (approximately) 42 (file position 1053) storing read block: ASSUMPTIONS storing read block: ASSUMPTIONS storing read block: MESQUITECHARMODELS storing read block: MESQUITE [Reading /<>/test/NTSValidOut/nhxtree.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: CODONS storing read block: SETS storing read block: ASSUMPTIONS storing read block: MESQUITECHARMODELS storing read block: MESQUITE [Reading /<>/test/NTSValidIn/charsets.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS storing read block: SETS storing read block: ASSUMPTIONS [Reading /<>/test/NTSValidOut/charsets.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS storing read block: SETS storing read block: ASSUMPTIONS [Reading /<>/test/NTSValidIn/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED [Reading /<>/test/NTSValidOut/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED [Reading /<>/test/NTSValidIn/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/NTSValidOut/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/NTSValidIn/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidOut/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/bglobin.nex" ../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") ../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/bglobin.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/bglobin.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/bglobin.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/anolis.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/anolis.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/anolis.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/anolis.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/characters.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/characters.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/characters.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/characters.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/basic-bush-dos.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/basic-bush-dos.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/basic-bush-dos.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/basic-bush-dos.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/nhxtree.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/nhxtree.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/nhxtree.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/nhxtree.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/charsets.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/charsets.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/charsets.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/charsets.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/unaligned.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/unaligned.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/unaligned.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/unaligned.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/protein.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/protein.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/protein.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/protein.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/basic-bush-unix.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/basic-bush-unix.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/basic-bush-unix.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/basic-bush-unix.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/basic-bush-mixed-line-endings.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/basic-bush-mixed-line-endings.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/basic-bush-mixed-line-endings.nex" [Reading /<>/test/NTSValidOut/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidIn/basic-rake.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: CODONS Warning: An * is ignored in a CHARSET command at line 67, column (approximately) 46 (file position 929) Warning: An * is ignored in a CHARSET command at line 68, column (approximately) 42 (file position 968) storing read block: ASSUMPTIONS storing read block: ASSUMPTIONS storing read block: MESQUITECHARMODELS storing read block: MESQUITE [Reading /<>/test/NTSValidOut/basic-rake.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: CODONS storing read block: SETS storing read block: ASSUMPTIONS storing read block: MESQUITECHARMODELS storing read block: MESQUITE [Reading /<>/test/NTSValidIn/paup_characters.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/NTSValidOut/paup_characters.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 188) storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/NTSValidIn/linktest.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 189) storing read block: TAXA Warning: Skipping command: blockid at line 27, column (approximately) 11 (file position 388) storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS Warning: Skipping unknown LINK subcommand: characters at line 61, column (approximately) 38 (file position 1551) storing read block: TREES Warning: Skipping unknown LINK subcommand: characters at line 71, column (approximately) 38 (file position 1745) storing read block: TREES storing implied block: ASSUMPTIONS storing implied block: ASSUMPTIONS storing read block: ASSUMPTIONS Warning: A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s). at line 90, column (approximately) 42 (file position 2360) storing read block: ASSUMPTIONS storing read block: ASSUMPTIONS [Reading /<>/test/NTSValidOut/linktest.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 168) storing read block: TAXA Warning: Skipping command: blockid at line 12, column (approximately) 13 (file position 341) storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: TREES storing read block: TREES storing read block: SETS storing read block: SETS storing read block: SETS Warning: A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s). at line 84, column (approximately) 20 (file position 2384) storing read block: SETS storing read block: SETS [Reading /<>/test/NTSValidIn/basic-bush-mac.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidOut/basic-bush-mac.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidIn/primates.nex ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/NTSValidOut/primates.nex ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/NTSValidIn/partitions.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: SETS storing read block: ASSUMPTIONS [Reading /<>/test/NTSValidOut/partitions.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: SETS storing read block: ASSUMPTIONS [Reading /<>/test/NTSValidIn/m.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS [Reading /<>/test/NTSValidOut/m.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: SETS [Reading /<>/test/NTSValidIn/notaxablock.nex ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 3, column (approximately) 13 (file position 32) storing implied block: TAXA storing read block: TREES [Reading /<>/test/NTSValidOut/notaxablock.nex ] Executing storing read block: TAXA storing read block: TREES [Reading /<>/test/NTSValidIn/kim.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES [Reading /<>/test/NTSValidOut/kim.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES [Reading /<>/test/NTSValidIn/replicase.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/basic-bush-mixed-line-endings.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/basic-rake.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/basic-rake.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/basic-rake.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/basic-rake.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/paup_characters.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/paup_characters.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/paup_characters.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/paup_characters.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/linktest.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/linktest.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/linktest.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/linktest.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/basic-bush-mac.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/basic-bush-mac.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/basic-bush-mac.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/basic-bush-mac.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/primates.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/primates.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/primates.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/primates.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/partitions.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/partitions.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/partitions.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/partitions.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/m.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/m.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/m.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/m.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/notaxablock.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/notaxablock.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/notaxablock.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/notaxablock.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/kim.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/kim.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/kim.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/kim.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/replicase.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/replicase.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/replicase.nex" [Reading /<>/test/NTSValidOut/replicase.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES [Reading /<>/test/NTSValidIn/treeswithouttaxa.nex ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 3, column (approximately) 10 (file position 26) storing implied block: TAXA storing read block: TREES [Reading /<>/test/NTSValidOut/treeswithouttaxa.nex ] Executing storing read block: TAXA storing read block: TREES [Reading /<>/test/NTSValidIn/t.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidOut/t.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES [Reading /<>/test/NTSValidIn/mdata.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: ASSUMPTIONS [Reading /<>/test/NTSValidOut/mdata.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: SETS [Reading /<>/test/NTSValidIn/dzmissing_bug.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: ASSUMPTIONS storing read block: MACCLADE [Reading /<>/test/NTSValidOut/dzmissing_bug.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS storing read block: MACCLADE [Reading /<>/test/NTSValidIn/notaxablock-quotes.nex ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 3, column (approximately) 7 (file position 26) storing implied block: TAXA storing read block: TREES [Reading /<>/test/NTSValidOut/notaxablock-quotes.nex ] Executing storing read block: TAXA storing read block: TREES [Reading /<>/test/NTSValidIn/adh.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES [Reading /<>/test/NTSValidOut/adh.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES [Reading /<>/test/NTSValidIn/associates.nex ] Executing storing read block: TAXA storing read block: TAXA storing read block: TAXAASSOCIATION [Reading /<>/test/NTSValidOut/associates.nex ] Executing storing read block: TAXA storing read block: TAXA storing read block: TAXAASSOCIATION [Reading /<>/test/NTSValidIn/distances.nex ] Executing storing read block: TAXA storing read block: DISTANCES [Reading /<>/test/NTSValidOut/distances.nex ] Executing storing read block: TAXA storing read block: DISTANCES [Reading /<>/test/NTSValidIn/cynmix.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES storing read block: MRBAYES [Reading /<>/test/NTSValidOut/cynmix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES storing read block: MRBAYES [Reading /<>/test/NTSValidIn/avian_ovomucoids.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/replicase.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/treeswithouttaxa.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/treeswithouttaxa.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/treeswithouttaxa.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/treeswithouttaxa.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/t.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/t.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/t.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/t.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/mdata.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/mdata.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/mdata.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/mdata.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/dzmissing_bug.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/dzmissing_bug.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/dzmissing_bug.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/dzmissing_bug.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/notaxablock-quotes.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/notaxablock-quotes.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/notaxablock-quotes.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/notaxablock-quotes.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/adh.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/adh.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/adh.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/adh.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/associates.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/associates.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/associates.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/associates.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/distances.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/distances.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/distances.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/distances.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/cynmix.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/cynmix.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/cynmix.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/cynmix.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/avian_ovomucoids.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/avian_ovomucoids.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/avian_ovomucoids.nex" [Reading /<>/test/NTSValidOut/avian_ovomucoids.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES [Reading /<>/test/NTSValidIn/parens_intree.tre ] Executing storing read block: TAXA storing read block: TREES [Reading /<>/test/NTSValidOut/parens_intree.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/avian_ovomucoids.nex "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidIn/parens_intree.tre" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidIn/parens_intree.tre "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/NTSValidOut/parens_intree.tre" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/NTSValidOut/parens_intree.tre /usr/bin/python3 ../../test/roundTripNCLTest.py -x ../../example/normalizer/NEXUSnormalizer ../../test/funkyValidIn ../../test/funkyValidOut [Reading /<>/test/funkyValidIn/choke.tre ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 5, column (approximately) 6 (file position 74) storing implied block: TAXA storing read block: TREES [Reading /<>/test/funkyValidOut/choke.tre ] Executing storing read block: TAXA storing read block: TREES "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/<>/test/funkyValidIn/choke.tre" ../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") ../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/funkyValidIn/choke.tre "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/<>/test/funkyValidOut/choke.tre" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/funkyValidOut/choke.tre /usr/bin/python3 ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut [Reading /<>/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/ExternalValidOut/dnarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/ExternalValidIn/aaphylip_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/ExternalValidOut/aaphylip_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/ExternalValidIn/aarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/ExternalValidOut/aarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/ExternalValidIn/relaxedphyliptree_q.phy ] Executing storing implied block: TAXA storing read block: TREES [Reading /<>/test/ExternalValidOut/relaxedphyliptree_q.phy ] Executing storing read block: TAXA storing read block: TREES [Reading /<>/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/ExternalValidIn/phyliptree_simple.phy ] Executing storing implied block: TAXA storing read block: TREES [Reading /<>/test/ExternalValidOut/phyliptree_simple.phy ] Executing storing read block: TAXA storing read block: TREES [Reading /<>/test/ExternalValidIn/aafasta_twoprot.fas ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/ExternalValidOut/aafasta_twoprot.fas ] Executing storing read block: TAXA storing read block: CHARACTERS [Reading /<>/test/ExternalValidIn/aaaln_twoprot_undec.aln ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/ExternalValidOut/aaaln_twoprot_undec.aln ] Executing storing read block: TAXA storing read block: CHARACTERS "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/<>/test/ExternalValidIn/dnarelaxedphylip_rana.phy" ../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") ../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/dnarelaxedphylip_rana.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/dnarelaxedphylip_rana.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/dnarelaxedphylip_rana.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/<>/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/aaphylipinterleaved_emboss.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/aaphylipinterleaved_emboss.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/<>/test/ExternalValidIn/aaphylip_emboss.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/aaphylip_emboss.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/aaphylip_emboss.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/aaphylip_emboss.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/<>/test/ExternalValidIn/aarelaxedphylip_rana.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/aarelaxedphylip_rana.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/aarelaxedphylip_rana.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/aarelaxedphylip_rana.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/<>/test/ExternalValidIn/relaxedphyliptree_q.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/relaxedphyliptree_q.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/relaxedphyliptree_q.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/relaxedphyliptree_q.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/<>/test/ExternalValidIn/dnarelaxedphylip_brana.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/dnarelaxedphylip_brana.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/dnarelaxedphylip_brana.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/dnarelaxedphylip_brana.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/<>/test/ExternalValidIn/phyliptree_simple.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/phyliptree_simple.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/phyliptree_simple.phy" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/phyliptree_simple.phy "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/<>/test/ExternalValidIn/aafasta_twoprot.fas" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/aafasta_twoprot.fas "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/aafasta_twoprot.fas" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/aafasta_twoprot.fas "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/<>/test/ExternalValidIn/aaaln_twoprot_undec.aln" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/aaaln_twoprot_undec.aln "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/aaaln_twoprot_undec.aln" ../../test/roundTripNCLTest.py : Call to[Reading /<>/test/ExternalValidIn/aaaln_twoprot.aln ] Executing storing implied block: TAXA storing read block: DATA [Reading /<>/test/ExternalValidOut/aaaln_twoprot.aln ] Executing storing read block: TAXA storing read block: CHARACTERS /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/aaaln_twoprot_undec.aln "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/<>/test/ExternalValidIn/aaaln_twoprot.aln" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidIn/aaaln_twoprot.aln "/<>/example/normalizer/NEXUSnormalizer" "-s2" "/<>/test/ExternalValidOut/aaaln_twoprot.aln" ../../test/roundTripNCLTest.py : Call to /<>/example/normalizer/NEXUSnormalizer succeeded for /<>/test/ExternalValidOut/aaaln_twoprot.aln /usr/bin/python3 ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn [Reading /<>/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy ] Executing Error: Illegal state code "q" found when reading site 2 for taxon grylioMVZ175945 at line 12, column (approximately) 28 (and file position 20065) [Reading /<>/test/ExternalInvalidIn/aarelaxedphylip_rana.phy ] Executing Error: Sequence longer than 1976 found for taxon temporariaDMH84R1. The character "o" was found, and will be ignored. If the file position of this error corresponds to sequences for the next taxon in the matrix, then that is an indication that the sequences for taxon temporariaDMH84R1 are too short. at line 3, column (approximately) 2 (and file position 2011) "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/<>/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy" "/<>/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/<>/test/ExternalInvalidIn/aarelaxedphylip_rana.phy" /usr/bin/python3 ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer /sbuild-nonexistent/.ncl_round_triprc does not exist. Test stepped skipped. make[4]: Leaving directory '/<>/example/normalizer' make[3]: Leaving directory '/<>/example/normalizer' Making check in ot-subtree make[3]: Entering directory '/<>/example/ot-subtree' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/ot-subtree' Making check in ot-tree-inspect make[3]: Entering directory '/<>/example/ot-tree-inspect' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/ot-tree-inspect' Making check in outdeg1count make[3]: Entering directory '/<>/example/outdeg1count' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/outdeg1count' Making check in patristic make[3]: Entering directory '/<>/example/patristic' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/patristic' Making check in phylobaseinterface make[3]: Entering directory '/<>/example/phylobaseinterface' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/phylobaseinterface' Making check in polytomy-count make[3]: Entering directory '/<>/example/polytomy-count' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/polytomy-count' Making check in splitsinfile make[3]: Entering directory '/<>/example/splitsinfile' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/splitsinfile' Making check in subsetter make[3]: Entering directory '/<>/example/subsetter' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/example/subsetter' Making check in translate make[3]: Entering directory '/<>/example/translate' make check-local make[4]: Entering directory '/<>/example/translate' /usr/bin/python3 ../../test/roundTripNCLTest.py -o ../../example/translate/NEXUStranslate ../../test/TranslateIn ../../test/TranslateOut [Reading /<>/test/TranslateIn/bglobin.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES [Reading /<>/test/TranslateIn/bglobinoof.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: CODONS "/<>/example/translate/NEXUStranslate" "-s2" "/<>/test/TranslateIn/bglobin.nex" ../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") ../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /<>/example/translate/NEXUStranslate succeeded for /<>/test/TranslateIn/bglobin.nex "/<>/example/translate/NEXUStranslate" "-s2" "/<>/test/TranslateIn/bglobinoof.nex" ../../test/roundTripNCLTest.py : Call to /<>/example/translate/NEXUStranslate succeeded for /<>/test/TranslateIn/bglobinoof.nex make[4]: Leaving directory '/<>/example/translate' make[3]: Leaving directory '/<>/example/translate' make[3]: Entering directory '/<>/example' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/example' make[2]: Leaving directory '/<>/example' Making check in test make[2]: Entering directory '/<>/test' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/test' make[2]: Entering directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/libncl-2.1.21\+git20190531.feceb81/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' Making install in ncl make[2]: Entering directory '/<>/ncl' make[3]: Entering directory '/<>/ncl' /bin/mkdir -p '/<>/debian/tmp/usr/lib/riscv64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/<>/debian/tmp/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /<>/debian/tmp/usr/lib/riscv64-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/riscv64-linux-gnu && { ln -s -f libncl.so.2.0.0 libncl.so.2 || { rm -f libncl.so.2 && ln -s libncl.so.2.0.0 libncl.so.2; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/riscv64-linux-gnu && { ln -s -f libncl.so.2.0.0 libncl.so || { rm -f libncl.so && ln -s libncl.so.2.0.0 libncl.so; }; }) libtool: install: /usr/bin/install -c .libs/libncl.lai /<>/debian/tmp/usr/lib/riscv64-linux-gnu/libncl.la libtool: install: /usr/bin/install -c .libs/libncl.a /<>/debian/tmp/usr/lib/riscv64-linux-gnu/libncl.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/riscv64-linux-gnu/libncl.a libtool: install: ranlib /<>/debian/tmp/usr/lib/riscv64-linux-gnu/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/riscv64-linux-gnu' /bin/mkdir -p '/<>/debian/tmp/usr/include/ncl' /usr/bin/install -c -m 644 ncl.h nxsallocatematrix.h nxsassumptionsblock.h nxsblock.cpp nxsblock.h nxscharactersblock.h nxscdiscretematrix.h nxscxxdiscretematrix.h nxsdatablock.h nxsdefs.h nxsdiscretedatum.h nxsdistancedatum.h nxsdistancesblock.h nxsexception.h nxsmultiformat.h nxspublicblocks.h nxsreader.h nxssetreader.h nxsstring.h nxstaxablock.h nxstaxaassociationblock.h nxstoken.h nxstreesblock.h nxsunalignedblock.h nxsutilcopy.h '/<>/debian/tmp/usr/include/ncl' make[3]: Leaving directory '/<>/ncl' make[2]: Leaving directory '/<>/ncl' Making install in example make[2]: Entering directory '/<>/example' Making install in basiccmdline make[3]: Entering directory '/<>/example/basiccmdline' make[4]: Entering directory '/<>/example/basiccmdline' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/basiccmdline' make[3]: Leaving directory '/<>/example/basiccmdline' Making install in check-taxo-nodes make[3]: Entering directory '/<>/example/check-taxo-nodes' make[4]: Entering directory '/<>/example/check-taxo-nodes' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/<>/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/checktaxonnodes /<>/debian/tmp/usr/bin/checktaxonnodes make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/check-taxo-nodes' make[3]: Leaving directory '/<>/example/check-taxo-nodes' Making install in compressor make[3]: Entering directory '/<>/example/compressor' make[4]: Entering directory '/<>/example/compressor' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/compressor' make[3]: Leaving directory '/<>/example/compressor' Making install in find-unsupported-edges make[3]: Entering directory '/<>/example/find-unsupported-edges' make[4]: Entering directory '/<>/example/find-unsupported-edges' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/<>/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/findunsupportededges /<>/debian/tmp/usr/bin/findunsupportededges make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/find-unsupported-edges' make[3]: Leaving directory '/<>/example/find-unsupported-edges' Making install in gapcode make[3]: Entering directory '/<>/example/gapcode' make[4]: Entering directory '/<>/example/gapcode' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/gapcode' make[3]: Leaving directory '/<>/example/gapcode' Making install in nclsimplest make[3]: Entering directory '/<>/example/nclsimplest' make[4]: Entering directory '/<>/example/nclsimplest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/nclsimplest' make[3]: Leaving directory '/<>/example/nclsimplest' Making install in ncltest make[3]: Entering directory '/<>/example/ncltest' make[4]: Entering directory '/<>/example/ncltest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/ncltest' make[3]: Leaving directory '/<>/example/ncltest' Making install in normalizer make[3]: Entering directory '/<>/example/normalizer' make[4]: Entering directory '/<>/example/normalizer' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/<>/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSnormalizer /<>/debian/tmp/usr/bin/NEXUSnormalizer libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSvalidator /<>/debian/tmp/usr/bin/NEXUSvalidator libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NCLconverter /<>/debian/tmp/usr/bin/NCLconverter make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/normalizer' make[3]: Leaving directory '/<>/example/normalizer' Making install in ot-subtree make[3]: Entering directory '/<>/example/ot-subtree' make[4]: Entering directory '/<>/example/ot-subtree' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c otsubtree '/<>/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/otsubtree /<>/debian/tmp/usr/bin/otsubtree make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/ot-subtree' make[3]: Leaving directory '/<>/example/ot-subtree' Making install in ot-tree-inspect make[3]: Entering directory '/<>/example/ot-tree-inspect' make[4]: Entering directory '/<>/example/ot-tree-inspect' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/<>/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/otTreeInspect /<>/debian/tmp/usr/bin/otTreeInspect make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/ot-tree-inspect' make[3]: Leaving directory '/<>/example/ot-tree-inspect' Making install in outdeg1count make[3]: Entering directory '/<>/example/outdeg1count' make[4]: Entering directory '/<>/example/outdeg1count' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c outdeg1count '/<>/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/riscv64-linux-gnu' libtool: install: /usr/bin/install -c .libs/outdeg1count /<>/debian/tmp/usr/bin/outdeg1count make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/outdeg1count' make[3]: Leaving directory '/<>/example/outdeg1count' Making install in patristic make[3]: Entering directory '/<>/example/patristic' make[4]: Entering directory '/<>/example/patristic' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/patristic' make[3]: Leaving directory '/<>/example/patristic' Making install in phylobaseinterface make[3]: Entering directory '/<>/example/phylobaseinterface' make[4]: Entering directory '/<>/example/phylobaseinterface' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/phylobaseinterface' make[3]: Leaving directory '/<>/example/phylobaseinterface' Making install in polytomy-count make[3]: Entering directory '/<>/example/polytomy-count' make[4]: Entering directory '/<>/example/polytomy-count' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/polytomy-count' make[3]: Leaving directory '/<>/example/polytomy-count' Making install in splitsinfile make[3]: Entering directory '/<>/example/splitsinfile' make[4]: Entering directory '/<>/example/splitsinfile' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/splitsinfile' make[3]: Leaving directory '/<>/example/splitsinfile' Making install in subsetter make[3]: Entering directory '/<>/example/subsetter' make[4]: Entering directory '/<>/example/subsetter' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/subsetter' make[3]: Leaving directory '/<>/example/subsetter' Making install in translate make[3]: Entering directory '/<>/example/translate' make[4]: Entering directory '/<>/example/translate' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example/translate' make[3]: Leaving directory '/<>/example/translate' make[3]: Entering directory '/<>/example' make[4]: Entering directory '/<>/example' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/example' make[3]: Leaving directory '/<>/example' make[2]: Leaving directory '/<>/example' Making install in test make[2]: Entering directory '/<>/test' make[3]: Entering directory '/<>/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>/test' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/debian/tmp/usr/lib/riscv64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 nclv2.1.pc '/<>/debian/tmp/usr/lib/riscv64-linux-gnu/pkgconfig' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/ncl/*.h" usr/include/ncl \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/riscv64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/libncl.so Library package automatic movement utility set -e install -d -m 755 debian/libncl-dev/usr/lib/riscv64-linux-gnu install -d -m 755 debian/libncl2/usr/lib/riscv64-linux-gnu mv debian/tmp/usr/lib/riscv64-linux-gnu/libncl.a debian/libncl-dev/usr/lib/riscv64-linux-gnu mv debian/tmp/usr/lib/riscv64-linux-gnu/libncl.la debian/libncl-dev/usr/lib/riscv64-linux-gnu || true mv debian/tmp/usr/lib/riscv64-linux-gnu/libncl.so debian/libncl-dev/usr/lib/riscv64-linux-gnu mv /<>/debian/tmp/usr/lib/riscv64-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/riscv64-linux-gnu mv /<>/debian/tmp/usr/lib/riscv64-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/riscv64-linux-gnu PKGDEV=libncl-dev PKGSHL=libncl2 install -d -m 755 debian/libncl-dev/usr/include/ncl mv debian/tmp/usr/include/ncl/*.h debian/libncl-dev/usr/include/ncl install -d -m 755 debian/libncl-dev/usr/lib/riscv64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libncl-dev/usr/lib/riscv64-linux-gnu/pkgconfig rm -f debian/tmp/usr/include/ncl/nxsblock.cpp make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libncl-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing libncl-dev (in debian/libncl-dev); do_strip: , oemstrip: pkgstriptranslations: processing libncl2 (in debian/libncl2); do_strip: , oemstrip: pkgstriptranslations: processing ncl-tools (in debian/ncl-tools); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libncl-dev/DEBIAN/control, package libncl-dev, directory debian/libncl-dev pkgstripfiles: processing control file: debian/ncl-tools/DEBIAN/control, package ncl-tools, directory debian/ncl-tools INFO: pkgstripfiles: waiting for lock (libncl-dev) ... Searching for duplicated docs in dependency libncl2... symlinking changelog.Debian.gz in ncl-tools to file in libncl2 INFO: pkgstripfiles: waiting for lock (libncl-dev) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package ncl-tools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20190531.feceb81-2build1_riscv64.deb'. INFO: pkgstripfiles: waiting for lock (libncl-dev) ... INFO: pkgstripfiles: waiting for lock (libncl-dev) ... pkgstripfiles: processing control file: debian/libncl2/DEBIAN/control, package libncl2, directory debian/libncl2 INFO: pkgstripfiles: waiting for lock (libncl-dev) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libncl2 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20190531.feceb81-2build1_riscv64.deb'. Searching for duplicated docs in dependency libncl2... symlinking changelog.Debian.gz in libncl-dev to file in libncl2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libncl-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20190531.feceb81-2build1_riscv64.deb'. INFO: pkgstriptranslations version 144 pkgstriptranslations: processing ncl-tools-dbgsym (in debian/.debhelper/ncl-tools/dbgsym-root); do_strip: , oemstrip: INFO: pkgstriptranslations version 144 pkgstriptranslations: processing libncl2-dbgsym (in debian/.debhelper/libncl2/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/ncl-tools/dbgsym-root/DEBIAN/control, package ncl-tools-dbgsym, directory debian/.debhelper/ncl-tools/dbgsym-root dpkg-deb: building package 'ncl-tools-dbgsym' in 'debian/.debhelper/scratch-space/build-ncl-tools/ncl-tools-dbgsym_2.1.21+git20190531.feceb81-2build1_riscv64.deb'. pkgstripfiles: processing control file: debian/.debhelper/libncl2/dbgsym-root/DEBIAN/control, package libncl2-dbgsym, directory debian/.debhelper/libncl2/dbgsym-root dpkg-deb: building package 'libncl2-dbgsym' in 'debian/.debhelper/scratch-space/build-libncl2/libncl2-dbgsym_2.1.21+git20190531.feceb81-2build1_riscv64.deb'. Renaming ncl-tools-dbgsym_2.1.21+git20190531.feceb81-2build1_riscv64.deb to ncl-tools-dbgsym_2.1.21+git20190531.feceb81-2build1_riscv64.ddeb Renaming libncl2-dbgsym_2.1.21+git20190531.feceb81-2build1_riscv64.deb to libncl2-dbgsym_2.1.21+git20190531.feceb81-2build1_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../libncl_2.1.21+git20190531.feceb81-2build1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-04-03T04:09:37Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ libncl_2.1.21+git20190531.feceb81-2build1_riscv64.changes: ---------------------------------------------------------- Format: 1.8 Date: Sun, 22 Mar 2020 16:46:15 +0100 Source: libncl Binary: libncl-dev libncl2 ncl-tools Architecture: riscv64 Version: 2.1.21+git20190531.feceb81-2build1 Distribution: focal Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: libncl-dev - NEXUS Class Library (static lib and header files) libncl2 - NEXUS Class Library ncl-tools - tools to deal with NEXUS files Changes: libncl (2.1.21+git20190531.feceb81-2build1) focal; urgency=medium . * No-change rebuild for libgcc-s1 package name change. 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binutils-riscv64-linux-gnu (= 2.34-5ubuntu1), bsdmainutils (= 11.1.2ubuntu3), bsdutils (= 1:2.34-0.1ubuntu8), build-essential (= 12.8ubuntu1), bzip2 (= 1.0.8-2), coreutils (= 8.30-3ubuntu2), cpp (= 4:9.3.0-1ubuntu2), cpp-9 (= 9.3.0-8ubuntu1), d-shlibs (= 0.89), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.10ubuntu1), debianutils (= 4.9.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.3-2), diffutils (= 1:3.7-3), dpkg (= 1.19.7ubuntu3), dpkg-dev (= 1.19.7ubuntu3), dwz (= 0.13-5), file (= 1:5.38-4), findutils (= 4.7.0-1ubuntu1), g++ (= 4:9.3.0-1ubuntu2), g++-9 (= 9.3.0-8ubuntu1), gcc (= 4:9.3.0-1ubuntu2), gcc-10-base (= 10-20200324-1ubuntu1), gcc-9 (= 9.3.0-8ubuntu1), gcc-9-base (= 9.3.0-8ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), gpgv (= 2.2.19-3ubuntu2), grep (= 3.4-1), groff-base (= 1.22.4-4build1), gzip (= 1.10-0ubuntu4), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-6), libapt-pkg6.0 (= 2.0.1), libarchive-zip-perl (= 1.67-2), libatomic1 (= 10-20200324-1ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2ubuntu6), libaudit1 (= 1:2.8.5-2ubuntu6), libbinutils (= 2.34-5ubuntu1), libblkid1 (= 2.34-0.1ubuntu8), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.31-0ubuntu6~riscv64.1), libc-dev-bin (= 2.31-0ubuntu6~riscv64.1), libc6 (= 2.31-0ubuntu6~riscv64.1), libc6-dev (= 2.31-0ubuntu6~riscv64.1), libcap-ng0 (= 0.7.9-2.1build1), libcc1-0 (= 10-20200324-1ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.10-10ubuntu4), libcrypt1 (= 1:4.4.10-10ubuntu4), libctf-nobfd0 (= 2.34-5ubuntu1), libctf0 (= 2.34-5ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu2), libdebconfclient0 (= 0.251ubuntu1), libdebhelper-perl (= 12.10ubuntu1), libdpkg-perl (= 1.19.7ubuntu3), libelf1 (= 0.176-1.1build1), libexpat1 (= 2.2.9-1build1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.6.3-2), libgcc-9-dev (= 9.3.0-8ubuntu1), libgcc-s1 (= 10-20200324-1ubuntu1), libgcc1 (= 1:10-20200324-1ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu1), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.1-1), libgmp10 (= 2:6.2.0+dfsg-4), libgnutls30 (= 3.6.11.1-2ubuntu2), libgomp1 (= 10-20200324-1ubuntu1), libgpg-error0 (= 1.37-1), libhogweed5 (= 3.5.1+really3.5.1-2), libicu66 (= 66.1-2ubuntu2), libidn2-0 (= 2.2.0-2), libisl22 (= 0.22.1-1), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.34-0.1ubuntu8), libmpc3 (= 1.1.0-1), libmpdec2 (= 2.4.2-3), libmpfr6 (= 4.0.2-1), libncursesw6 (= 6.2-0ubuntu2), libnettle7 (= 3.5.1+really3.5.1-2), libp11-kit0 (= 0.23.20-1build1), libpam-modules (= 1.3.1-5ubuntu4), libpam-modules-bin (= 1.3.1-5ubuntu4), libpam-runtime (= 1.3.1-5ubuntu4), libpam0g (= 1.3.1-5ubuntu4), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12build1), libperl5.30 (= 5.30.0-9build1), libpipeline1 (= 1.5.2-2build1), libpython3-stdlib (= 3.8.2-0ubuntu2), libpython3.8-minimal (= 3.8.2-1ubuntu1), libpython3.8-stdlib (= 3.8.2-1ubuntu1), libreadline8 (= 8.0-4), libselinux1 (= 3.0-1build2), libsemanage-common (= 3.0-1build2), libsemanage1 (= 3.0-1build2), libsepol1 (= 3.0-1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1ubuntu8), libsqlite3-0 (= 3.31.1-4), libssl1.1 (= 1.1.1d-2ubuntu6), libstdc++-9-dev (= 9.3.0-8ubuntu1), libstdc++6 (= 10-20200324-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 244.3-1ubuntu1), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2-0ubuntu2), libtool (= 2.4.6-13), libuchardet0 (= 0.0.6-3build1), libudev1 (= 244.3-1ubuntu1), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1ubuntu8), libxml2 (= 2.9.10+dfsg-4build1), libzstd1 (= 1.4.4+dfsg-3), linux-libc-dev (= 5.4.0-21.25), login (= 1:4.8.1-1ubuntu3), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), mime-support (= 3.64ubuntu1), ncurses-base (= 6.2-0ubuntu2), ncurses-bin (= 6.2-0ubuntu2), passwd (= 1:4.8.1-1ubuntu3), patch (= 2.7.6-6), perl (= 5.30.0-9build1), perl-base (= 5.30.0-9build1), perl-modules-5.30 (= 5.30.0-9build1), po-debconf (= 1.0.21), python3 (= 3.8.2-0ubuntu2), python3-minimal (= 3.8.2-0ubuntu2), python3.8 (= 3.8.2-1ubuntu1), python3.8-minimal (= 3.8.2-1ubuntu1), readline-common (= 8.0-4), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-2.1ubuntu1), tar (= 1.30+dfsg-7), tzdata (= 2019c-3ubuntu1), ubuntu-keyring (= 2020.02.11.1), util-linux (= 2.34-0.1ubuntu8), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1584891975" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libncl-dev_2.1.21+git20190531.feceb81-2build1_riscv64.deb --------------------------------------------------------- new Debian package, version 2.0. size 2281808 bytes: control archive=1532 bytes. 800 bytes, 20 lines control 1887 bytes, 28 lines md5sums Package: libncl-dev Source: libncl Version: 2.1.21+git20190531.feceb81-2build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 24763 Depends: libncl2 (= 2.1.21+git20190531.feceb81-2build1) Section: libdevel Priority: optional Homepage: https://github.com/mtholder/ncl Description: NEXUS Class Library (static lib and header files) The NEXUS Class Library is a C++ library for parsing NEXUS files. . The NEXUS file format is widely used in bioinformatics. Several popular phylogenetic programs such as Paup, MrBayes, Mesquite, and MacClade use this format. . This package contains the static library and header files of the NEXUS library. drwxr-xr-x root/root 0 2020-03-22 15:46 ./ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/include/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/include/ncl/ -rw-r--r-- root/root 2384 2020-03-22 15:46 ./usr/include/ncl/ncl.h -rw-r--r-- root/root 5928 2020-03-22 15:46 ./usr/include/ncl/nxsallocatematrix.h -rw-r--r-- root/root 14934 2020-03-22 15:46 ./usr/include/ncl/nxsassumptionsblock.h -rw-r--r-- root/root 15451 2020-03-22 15:46 ./usr/include/ncl/nxsblock.h -rw-r--r-- root/root 3814 2020-03-22 15:46 ./usr/include/ncl/nxscdiscretematrix.h -rw-r--r-- root/root 77971 2020-03-22 15:46 ./usr/include/ncl/nxscharactersblock.h -rw-r--r-- root/root 11249 2020-03-22 15:46 ./usr/include/ncl/nxscxxdiscretematrix.h -rw-r--r-- root/root 2145 2020-03-22 15:46 ./usr/include/ncl/nxsdatablock.h -rw-r--r-- root/root 4059 2020-03-22 15:46 ./usr/include/ncl/nxsdefs.h -rw-r--r-- root/root 2098 2020-03-22 15:46 ./usr/include/ncl/nxsdiscretedatum.h -rw-r--r-- root/root 1328 2020-03-22 15:46 ./usr/include/ncl/nxsdistancedatum.h -rw-r--r-- root/root 7403 2020-03-22 15:46 ./usr/include/ncl/nxsdistancesblock.h -rw-r--r-- root/root 3060 2020-03-22 15:46 ./usr/include/ncl/nxsexception.h -rw-r--r-- root/root 10912 2020-03-22 15:46 ./usr/include/ncl/nxsmultiformat.h -rw-r--r-- root/root 30636 2020-03-22 15:46 ./usr/include/ncl/nxspublicblocks.h -rw-r--r-- root/root 26955 2020-03-22 15:46 ./usr/include/ncl/nxsreader.h -rw-r--r-- root/root 4284 2020-03-22 15:46 ./usr/include/ncl/nxssetreader.h -rw-r--r-- root/root 21693 2020-03-22 15:46 ./usr/include/ncl/nxsstring.h -rw-r--r-- root/root 4646 2020-03-22 15:46 ./usr/include/ncl/nxstaxaassociationblock.h -rw-r--r-- root/root 16886 2020-03-22 15:46 ./usr/include/ncl/nxstaxablock.h -rw-r--r-- root/root 31363 2020-03-22 15:46 ./usr/include/ncl/nxstoken.h -rw-r--r-- root/root 35765 2020-03-22 15:46 ./usr/include/ncl/nxstreesblock.h -rw-r--r-- root/root 10644 2020-03-22 15:46 ./usr/include/ncl/nxsunalignedblock.h -rw-r--r-- root/root 9167 2020-03-22 15:46 ./usr/include/ncl/nxsutilcopy.h drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/lib/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/ -rw-r--r-- root/root 24973296 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/libncl.a -rw-r--r-- root/root 937 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/libncl.la lrwxrwxrwx root/root 0 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/libncl.so -> libncl.so.2.0.0 drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 306 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/pkgconfig/nclv2.1.pc drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/doc/libncl-dev/ lrwxrwxrwx root/root 0 2020-03-22 15:46 ./usr/share/doc/libncl-dev/changelog.Debian.gz -> ../libncl2/changelog.Debian.gz -rw-r--r-- root/root 1157 2019-12-16 07:33 ./usr/share/doc/libncl-dev/copyright libncl2_2.1.21+git20190531.feceb81-2build1_riscv64.deb ------------------------------------------------------ new Debian package, version 2.0. size 355428 bytes: control archive=948 bytes. 737 bytes, 19 lines control 218 bytes, 3 lines md5sums 49 bytes, 1 lines shlibs 73 bytes, 2 lines triggers Package: libncl2 Source: libncl Version: 2.1.21+git20190531.feceb81-2build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 973 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.0), libstdc++6 (>= 9) Section: libs Priority: optional Homepage: https://github.com/mtholder/ncl Description: NEXUS Class Library The NEXUS Class Library is a C++ library for parsing NEXUS files. . The NEXUS file format is widely used in bioinformatics. Several popular phylogenetic programs such as Paup, MrBayes, Mesquite, and MacClade use this format. . This package contains the dynamic NEXUS library. drwxr-xr-x root/root 0 2020-03-22 15:46 ./ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/lib/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/ lrwxrwxrwx root/root 0 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/libncl.so.2 -> libncl.so.2.0.0 -rw-r--r-- root/root 981976 2020-03-22 15:46 ./usr/lib/riscv64-linux-gnu/libncl.so.2.0.0 drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/doc/libncl2/ -rw-r--r-- root/root 918 2020-03-22 15:46 ./usr/share/doc/libncl2/changelog.Debian.gz -rw-r--r-- root/root 1157 2019-12-16 07:33 ./usr/share/doc/libncl2/copyright ncl-tools_2.1.21+git20190531.feceb81-2build1_riscv64.deb -------------------------------------------------------- new Debian package, version 2.0. size 173372 bytes: control archive=1108 bytes. 743 bytes, 17 lines control 740 bytes, 12 lines md5sums Package: ncl-tools Source: libncl Version: 2.1.21+git20190531.feceb81-2build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 809 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.0), libncl2 (>= 2.1.21+git20190531.feceb81), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: https://github.com/mtholder/ncl Description: tools to deal with NEXUS files The NEXUS Class Library is a C++ library for parsing NEXUS files. . The NEXUS file format is widely used in bioinformatics. Several popular phylogenetic programs such as Paup, MrBayes, Mesquite, and MacClade use this format. drwxr-xr-x root/root 0 2020-03-22 15:46 ./ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/bin/ -rwxr-xr-x root/root 212616 2020-03-22 15:46 ./usr/bin/NCLconverter -rwxr-xr-x root/root 76952 2020-03-22 15:46 ./usr/bin/NEXUSnormalizer -rwxr-xr-x root/root 76952 2020-03-22 15:46 ./usr/bin/NEXUSvalidator -rwxr-xr-x root/root 93200 2020-03-22 15:46 ./usr/bin/checktaxonnodes -rwxr-xr-x root/root 109672 2020-03-22 15:46 ./usr/bin/findunsupportededges -rwxr-xr-x root/root 81000 2020-03-22 15:46 ./usr/bin/otTreeInspect -rwxr-xr-x root/root 76840 2020-03-22 15:46 ./usr/bin/otsubtree -rwxr-xr-x root/root 76776 2020-03-22 15:46 ./usr/bin/outdeg1count drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/doc/ncl-tools/ lrwxrwxrwx root/root 0 2020-03-22 15:46 ./usr/share/doc/ncl-tools/changelog.Debian.gz -> ../libncl2/changelog.Debian.gz -rw-r--r-- root/root 1157 2019-12-16 07:33 ./usr/share/doc/ncl-tools/copyright drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/man/ drwxr-xr-x root/root 0 2020-03-22 15:46 ./usr/share/man/man1/ -rw-r--r-- root/root 1674 2020-03-22 15:46 ./usr/share/man/man1/NCLconverter.1.gz -rw-r--r-- root/root 1094 2020-03-22 15:46 ./usr/share/man/man1/NEXUSnormalizer.1.gz -rw-r--r-- root/root 1054 2020-03-22 15:46 ./usr/share/man/man1/NEXUSvalidator.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 679976 Build-Time: 3746 Distribution: focal Host Architecture: riscv64 Install-Time: 145 Job: libncl_2.1.21+git20190531.feceb81-2build1.dsc Machine Architecture: riscv64 Package: libncl Package-Time: 3924 Source-Version: 2.1.21+git20190531.feceb81-2build1 Space: 679976 Status: successful Version: 2.1.21+git20190531.feceb81-2build1 -------------------------------------------------------------------------------- Finished at 2020-04-03T04:09:37Z Build needed 01:05:24, 679976k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19106285 Scanning for processes to kill in build PACKAGEBUILD-19106285 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19106285 Stopping target for build PACKAGEBUILD-19106285 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19106285 Removing build PACKAGEBUILD-19106285