I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 7 14:33:28 +14 2023 I: pbuilder-time-stamp: 1691368408 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libncl_2.1.21+git20190531.feceb81-3.dsc] I: copying [./libncl_2.1.21+git20190531.feceb81.orig.tar.xz] I: copying [./libncl_2.1.21+git20190531.feceb81-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.xz_y15mM/trustedkeys.kbx': General error gpgv: Signature made Fri Jul 24 03:04:01 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libncl_2.1.21+git20190531.feceb81-3.dsc dpkg-source: info: extracting libncl in libncl-2.1.21+git20190531.feceb81 dpkg-source: info: unpacking libncl_2.1.21+git20190531.feceb81.orig.tar.xz dpkg-source: info: unpacking libncl_2.1.21+git20190531.feceb81-3.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/677841/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Aug 7 14:33 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/677841/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/677841/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=d8db904a8bfc4841b5c70234f9b4a5f0 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=677841 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.LGpoA4YV/pbuilderrc_1WJQ --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LGpoA4YV/b2 --logfile b2/build.log libncl_2.1.21+git20190531.feceb81-3.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 21 2022 more -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 9 Aug 7 14:33 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 21 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/677841/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19707 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 23.8 MB of archives. After unpacking 88.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 d-shlibs all 0.98 [17.9 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Fetched 23.8 MB in 1s (35.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19707 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20574 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20995 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/677841/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/677841/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/libncl-2.1.21+git20190531.feceb81/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libncl_2.1.21+git20190531.feceb81-3_source.changes dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20190531.feceb81-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' dh_clean find . -name ".roundTripNCL*" -delete make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf 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 '/build/libncl-2.1.21+git20190531.feceb81' dh_auto_configure -- --with-constfuncs=yes ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-constfuncs=yes 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 '2222' is supported by ustar format... yes checking whether GID '2222' 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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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... 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(cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... 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(cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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... (cached) yes checking for alarm... yes checking for working mktime... yes checking for working strtod... yes checking for memmove... yes checking for strchr... yes checking for strtol... yes checking for python3... /usr/bin/python3 checking python3 module: subprocess... yes checking whether make sets $(MAKE)... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating example/Makefile config.status: creating example/basiccmdline/Makefile config.status: creating example/check-taxo-nodes/Makefile config.status: creating example/compressor/Makefile config.status: creating example/find-unsupported-edges/Makefile config.status: creating example/gapcode/Makefile config.status: creating example/ot-subtree/Makefile config.status: creating example/ot-tree-inspect/Makefile config.status: creating example/nclsimplest/Makefile config.status: creating example/ncltest/Makefile config.status: creating example/normalizer/Makefile config.status: creating example/patristic/Makefile config.status: creating example/phylobaseinterface/Makefile config.status: creating example/polytomy-count/Makefile config.status: creating example/outdeg1count/Makefile config.status: creating example/splitsinfile/Makefile config.status: creating example/subsetter/Makefile config.status: creating example/translate/Makefile config.status: creating ncl/Makefile config.status: creating test/Makefile config.status: creating nclv2.1.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' dh_auto_build make -j15 make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' make all-recursive make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' Making all in ncl make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o 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'/build/libncl-2.1.21+git20190531.feceb81/example/patristic' 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=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o patristic.o patristic.cpp /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic' Making all in phylobaseinterface make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLInterface.o NCLInterface.cpp /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface' Making all in polytomy-count make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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=/build/libncl-2.1.21+git20190531.feceb81=. -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/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count' Making all in splitsinfile make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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=/build/libncl-2.1.21+git20190531.feceb81=. -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=/build/libncl-2.1.21+git20190531.feceb81=. -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=/build/libncl-2.1.21+git20190531.feceb81=. -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=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -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=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -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 '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile' Making all in subsetter make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSsubsetter-subsetter.o `test -f 'subsetter.cpp' || echo './'`subsetter.cpp /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter' Making all in translate make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStranslate-translateNuc.o `test -f 'translateNuc.cpp' || echo './'`translateNuc.cpp /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example' Making all in test make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/test' make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' dh_auto_test make -j15 check VERBOSE=1 make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' Making check in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' Making check in example make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example' Making check in basiccmdline make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline' Making check in check-taxo-nodes make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' Making check in compressor make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor' Making check in find-unsupported-edges make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' Making check in gapcode make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode' Making check in nclsimplest make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest' Making check in ncltest make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest' make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest' /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/ncltest/ncltest ../../test/OldValidIn ../../test/OldValidOut "/build/libncl-2.1.21+git20190531.feceb81/example/ncltest/ncltest" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/OldValidIn/m.nex" [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS /build/libncl-2.1.21+git20190531.feceb81/example/ncltest/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/ncltest/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/ncltest/ncltest succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/OldValidIn/m.nex "/build/libncl-2.1.21+git20190531.feceb81/example/ncltest/ncltest" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/OldValidOut/m.nex" [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/ncltest/ncltest succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/OldValidOut/m.nex make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest' Making check in normalizer make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/characters.nex ../../test/data "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/data/characters.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/data/characters.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/data/characters.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/data/characters.nex /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/sample.tre ../../test/data "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/data/sample.tre" [Reading /build/libncl-2.1.21+git20190531.feceb81/data/sample.tre ] Executing storing read block: PAUP storing read block: TAXA storing read block: TREES /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/data/sample.tre "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/data/sample.tre" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/data/sample.tre ] Executing storing read block: PAUP storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/data/sample.tre /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/nhxtree.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/nhxtree.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/nhxtree.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/nhxtree.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: SETS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: SETS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/linktest.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/linktest.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/linktest.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/linktest.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: ASSUMPTIONS storing read block: MACCLADE ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS storing read block: MACCLADE ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex ] Executing storing read block: TAXA storing read block: DISTANCES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex ] Executing storing read block: TAXA storing read block: DISTANCES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/characters.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/characters.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/characters.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/characters.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mac.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mac.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mac.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mac.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mac.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mac.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-dos.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-dos.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-dos.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-dos.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-dos.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-dos.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/associates.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/associates.nex ] Executing storing read block: TAXA storing read block: TAXA storing read block: TAXAASSOCIATION ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/associates.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/associates.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/associates.nex ] Executing storing read block: TAXA storing read block: TAXA storing read block: TAXAASSOCIATION ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/associates.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/parens_intree.tre" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/parens_intree.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/parens_intree.tre "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/parens_intree.tre" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/parens_intree.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/parens_intree.tre /usr/bin/python3 ../../test/roundTripNCLTest.py -x ../../example/normalizer/NEXUSnormalizer ../../test/funkyValidIn ../../test/funkyValidOut "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/libncl-2.1.21+git20190531.feceb81/test/funkyValidIn/choke.tre" [Reading /build/libncl-2.1.21+git20190531.feceb81/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 /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/funkyValidIn/choke.tre "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/libncl-2.1.21+git20190531.feceb81/test/funkyValidOut/choke.tre" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/funkyValidOut/choke.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/funkyValidOut/choke.tre /usr/bin/python3 ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy ] Executing storing implied block: TAXA storing read block: TREES /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/phyliptree_simple.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/phyliptree_simple.phy ] Executing storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/phyliptree_simple.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/phyliptree_simple.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/phyliptree_simple.phy ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/phyliptree_simple.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot.aln" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot.aln ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot.aln "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot.aln" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot.aln ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot.aln /usr/bin/python3 ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/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) "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalInvalidIn/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/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) /usr/bin/python3 ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer /build/libncl-2.1.21+git20190531.feceb81/debian/.debhelper/generated/_source/home/.ncl_round_triprc does not exist. Test stepped skipped. make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' Making check in ot-subtree make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' Making check in ot-tree-inspect make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' Making check in outdeg1count make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' Making check in patristic make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic' Making check in phylobaseinterface make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface' Making check in polytomy-count make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count' Making check in splitsinfile make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile' Making check in subsetter make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter' Making check in translate make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate' make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate' /usr/bin/python3 ../../test/roundTripNCLTest.py -o ../../example/translate/NEXUStranslate ../../test/TranslateIn ../../test/TranslateOut "/build/libncl-2.1.21+git20190531.feceb81/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobinoof.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobinoof.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: CODONS /build/libncl-2.1.21+git20190531.feceb81/example/translate/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/translate/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobinoof.nex "/build/libncl-2.1.21+git20190531.feceb81/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobin.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobin.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobin.nex make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate' make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example' Making check in test make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/test' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/test' make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/libncl-2.1.21\+git20190531.feceb81/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' Making install in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-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 /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-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 /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.la libtool: install: /usr/bin/install -c .libs/libncl.a /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.a libtool: install: chmod 644 /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.a libtool: install: ranlib /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/include/ncl' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' Making install in example make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example' Making install in basiccmdline make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline' Making install in check-taxo-nodes make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/checktaxonnodes /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/checktaxonnodes make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' Making install in compressor make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/compressor' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor' Making install in find-unsupported-edges make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/findunsupportededges /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/findunsupportededges make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' Making install in gapcode make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode' Making install in nclsimplest make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest' Making install in ncltest make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest' Making install in normalizer make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSnormalizer /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/NEXUSnormalizer libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSvalidator /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/NEXUSvalidator libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NCLconverter /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/NCLconverter make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' Making install in ot-subtree make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/otsubtree /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/otsubtree make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' Making install in ot-tree-inspect make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/otTreeInspect /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/otTreeInspect make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' Making install in outdeg1count make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/outdeg1count /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/outdeg1count make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' Making install in patristic make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/patristic' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic' Making install in phylobaseinterface make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface' Making install in polytomy-count make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count' Making install in splitsinfile make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile' Making install in subsetter make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter' Making install in translate make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example/translate' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate' make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/example' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example' Making install in test make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/test' make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 '/build/libncl-2.1.21+git20190531.feceb81/test' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/test' make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 nclv2.1.pc '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' debian/rules override_dh_install make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' 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/x86_64-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/x86_64-linux-gnu install -d -m 755 debian/libncl2/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libncl.a debian/libncl-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libncl.la debian/libncl-dev/usr/lib/x86_64-linux-gnu || true mv debian/tmp/usr/lib/x86_64-linux-gnu/libncl.so debian/libncl-dev/usr/lib/x86_64-linux-gnu mv /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/x86_64-linux-gnu mv /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/x86_64-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/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libncl-dev/usr/lib/x86_64-linux-gnu/pkgconfig rm -f debian/tmp/usr/include/ncl/nxsblock.cpp make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libncl-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20190531.feceb81-3_amd64.deb'. dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20190531.feceb81-3_amd64.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20190531.feceb81-3_amd64.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20190531.feceb81-3_amd64.deb'. dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20190531.feceb81-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libncl_2.1.21+git20190531.feceb81-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/677841/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/677841/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/677841 and its subdirectories I: Current time: Mon Aug 7 14:40:22 +14 2023 I: pbuilder-time-stamp: 1691368822