Tue Nov 3 19:47:04 UTC 2020 I: starting to build libncl/buster/arm64 on jenkins on '2020-11-03 19:46' Tue Nov 3 19:47:04 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_2/4071/console.log Tue Nov 3 19:47:04 UTC 2020 I: Downloading source for buster/libncl=2.1.21+git20180827.c71b264-2 --2020-11-03 19:47:04-- http://deb.debian.org/debian/pool/main/libn/libncl/libncl_2.1.21+git20180827.c71b264-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2180 (2.1K) Saving to: ‘libncl_2.1.21+git20180827.c71b264-2.dsc’ 0K .. 100% 172M=0s 2020-11-03 19:47:04 (172 MB/s) - ‘libncl_2.1.21+git20180827.c71b264-2.dsc’ saved [2180/2180] Tue Nov 3 19:47:04 UTC 2020 I: libncl_2.1.21+git20180827.c71b264-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libncl Binary: ncl-tools, libncl2, libncl-dev Architecture: any Version: 2.1.21+git20180827.c71b264-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/mtholder/ncl Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/libncl Vcs-Git: https://salsa.debian.org/med-team/libncl.git Build-Depends: debhelper (>= 11~), d-shlibs, python Package-List: libncl-dev deb libdevel optional arch=any libncl2 deb libs optional arch=any ncl-tools deb science optional arch=any Checksums-Sha1: 677f811bdc2ff210c930bac8a133cc3101fd80e5 544104 libncl_2.1.21+git20180827.c71b264.orig.tar.xz 76bada951f523f932a14342f70047f3e86975a18 17756 libncl_2.1.21+git20180827.c71b264-2.debian.tar.xz Checksums-Sha256: 0881732e1bfec59ff088e4b8055844f046a3341aad67ea0ff63f3f4f5d46da0b 544104 libncl_2.1.21+git20180827.c71b264.orig.tar.xz 6e05f128a71d028cba9b8461358f5570544afbc06d65573b107cd0f024a15d98 17756 libncl_2.1.21+git20180827.c71b264-2.debian.tar.xz Files: ae50aea2791ebf4cf72e6dfe5f86663b 544104 libncl_2.1.21+git20180827.c71b264.orig.tar.xz 32e42d490a3d227b78f7e654c2e697ff 17756 libncl_2.1.21+git20180827.c71b264-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlyBYFARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHWAA//Ra4keU9Pvpwjx9Qh5NYq84Ptlgz06ajv q2xIwcmkt5myId+EITrvkPNuEi8Bmn0m5L1t/2G1MGz4wU69gQBkVphCr/LuTGed O1Ol+ml5qiYrH50VytzZ9fUVe3LmBWzyDbo/o2KAua3wlx2HqJcf37a4Fr3OrVyI pxLUkcdrug1cpImgOK4PezZXFsW6eHW6Bt9apGHzwepKy26DhzHYrkCswMViIxvP vgClSsCita92fRhJZYlWzfAvGL4i77ylfMBiuUdBeeqHRG5Ay9k8X7+xavXbT4vw Dg7+Y3JHVZIqnpFnWUqF98MNpgEeO7sjy5X02ex7NcGV5+u9drLsDnKKGFcKcIZ6 Irohq9fw5V5VtHqMIDbKKQ9jowVAzeDmrWbp17zbOCZycYFl6WFKUEzTDk/Bb38/ zEKlWCln3GavVBjp4T1w+E0JpMx8jDyf9yMYY4msolwCZ9Qsl/dEdLQOWoo5Lpzm W6y1tgZHQDdcerY9/t3WB7Sm/KTTrk+8+e8RkCHC4ojVjUIIw/QbCTiyq+fBhakJ LkuHjQLPTguKHjTbbI16fwdbtV3poL/o1PSj3ePuA/6P1dmSIq5fWdq++tlcylWk d+yhoclnMqGvSzk/aZVhHrlX2+IZbzCCwxfUTk4olpBjJCsn+I6iDLeMLtA8OFBF YyDL+Bl5Z/M= =PMh2 -----END PGP SIGNATURE----- Tue Nov 3 19:47:04 UTC 2020 I: Checking whether the package is not for us Tue Nov 3 19:47:04 UTC 2020 I: Starting 1st build on remote node codethink9-arm64.debian.net. Tue Nov 3 19:47:04 UTC 2020 I: Preparing to do remote build '1' on codethink9-arm64.debian.net. Tue Nov 3 19:55:30 UTC 2020 I: Deleting $TMPDIR on codethink9-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 6 14:10:13 -12 2021 I: pbuilder-time-stamp: 1638843013 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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+git20180827.c71b264-2.dsc] I: copying [./libncl_2.1.21+git20180827.c71b264.orig.tar.xz] I: copying [./libncl_2.1.21+git20180827.c71b264-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Mar 7 06:17:52 2019 -12 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+git20180827.c71b264-2.dsc dpkg-source: info: extracting libncl in libncl-2.1.21+git20180827.c71b264 dpkg-source: info: unpacking libncl_2.1.21+git20180827.c71b264.orig.tar.xz dpkg-source: info: unpacking libncl_2.1.21+git20180827.c71b264-2.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3893/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3893' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.iZo1X8IeHO/pbuilderrc_UAiY --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.iZo1X8IeHO/b1 --logfile b1/build.log libncl_2.1.21+git20180827.c71b264-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink9-arm64 4.4.0-190-generic #220-Ubuntu SMP Fri Aug 28 23:03:33 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Nov 23 02:49 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/3893/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: arm64 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 (>= 11~), d-shlibs, python dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 24.4 MB of archives. After unpacking 90.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 d-shlibs all 0.84 [17.2 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Fetched 24.4 MB in 1s (17.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:arm64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. 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Setting up d-shlibs (0.84) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:arm64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/libncl-2.1.21+git20180827.c71b264/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20180827.c71b264-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' dh_clean find . -name ".roundTripNCL*" -delete make[1]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' debian/rules build dh build 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+git20180827.c71b264' dh_auto_configure -- --with-constfuncs=yes ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-constfuncs=yes configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' 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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C++ compiler works... yes checking for ANSI C header files... (cached) yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for inline... inline checking whether struct tm is in sys/time.h or time.h... time.h checking whether time.h and sys/time.h may both be included... yes checking for sys/time.h... yes checking for unistd.h... (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 python... /usr/bin/python checking python 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 configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' dh_auto_build make -j8 make[1]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' make all-recursive make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' Making all in ncl make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' /bin/bash ../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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong 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-fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' Making all in ot-subtree make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' 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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otsubtree-otsubtree.o `test -f 'otsubtree.cpp' || echo './'`otsubtree.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' Making all in ot-tree-inspect make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' 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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otTreeInspect-ot_tree_inspect.o `test -f 'ot_tree_inspect.cpp' || echo './'`ot_tree_inspect.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' Making all in outdeg1count make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' 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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o outdeg1count-outdeg1count.o `test -f 'outdeg1count.cpp' || echo './'`outdeg1count.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' Making all in patristic make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o patristic.o patristic.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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+git20180827.c71b264/example/patristic' Making all in phylobaseinterface make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLInterface.o NCLInterface.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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+git20180827.c71b264/example/phylobaseinterface' Making all in polytomy-count make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o polytomycount-polytomy_count.o `test -f 'polytomy_count.cpp' || echo './'`polytomy_count.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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+git20180827.c71b264/example/polytomy-count' Making all in splitsinfile make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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+git20180827.c71b264/example/splitsinfile' Making all in subsetter make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSsubsetter-subsetter.o `test -f 'subsetter.cpp' || echo './'`subsetter.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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+git20180827.c71b264/example/subsetter' Making all in translate make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStranslate-translateNuc.o `test -f 'translateNuc.cpp' || echo './'`translateNuc.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -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+git20180827.c71b264/example/translate' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example' Making all in test make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/test' make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' make[1]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' dh_auto_test make -j8 check VERBOSE=1 make[1]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' Making check in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' Making check in example make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example' Making check in basiccmdline make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' Making check in check-taxo-nodes make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' Making check in compressor make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' Making check in find-unsupported-edges make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' Making check in gapcode make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' Making check in nclsimplest make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' Making check in ncltest make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' /usr/bin/python ../../test/roundTripNCLTest.py ../../example/ncltest/ncltest ../../test/OldValidIn ../../test/OldValidOut "/build/libncl-2.1.21+git20180827.c71b264/example/ncltest/ncltest" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/OldValidIn/m.nex" [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/ncltest/ncltest succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/OldValidIn/m.nex "/build/libncl-2.1.21+git20180827.c71b264/example/ncltest/ncltest" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/ncltest/ncltest succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/OldValidOut/m.nex make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' Making check in normalizer make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' /usr/bin/python ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/characters.nex ../../test/data "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/data/characters.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/data/characters.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/data/characters.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/data/characters.nex /usr/bin/python ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/sample.tre ../../test/data "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/data/sample.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/data/sample.tre "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/data/sample.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/data/sample.tre /usr/bin/python ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/treeswithouttaxa.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/treeswithouttaxa.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/t.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/t.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/t.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/t.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/replicase.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/replicase.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/replicase.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/replicase.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/paup_characters.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/paup_characters.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/paup_characters.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/paup_characters.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/partitions.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/partitions.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/partitions.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/partitions.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock-quotes.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock-quotes.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/nhxtree.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/nhxtree.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/nhxtree.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/nhxtree.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/mdata.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/mdata.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/mdata.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/mdata.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/m.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/m.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/m.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/m.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/linktest.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/linktest.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/linktest.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/linktest.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/kim.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/kim.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/kim.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/kim.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/dzmissing_bug.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/dzmissing_bug.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/dzmissing_bug.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/dzmissing_bug.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex ] Executing storing read block: TAXA storing read block: DISTANCES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex ] Executing storing read block: TAXA storing read block: DISTANCES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/cynmix.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/cynmix.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/cynmix.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/cynmix.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/charsets.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/charsets.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/charsets.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/charsets.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/characters.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/characters.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/characters.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/characters.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/bglobin.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/bglobin.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/bglobin.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/bglobin.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-rake.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-rake.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-rake.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-rake.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-unix.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-unix.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-unix.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-unix.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mixed-line-endings.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mixed-line-endings.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mixed-line-endings.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mixed-line-endings.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mac.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mac.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mac.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mac.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-dos.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-dos.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-dos.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-dos.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/adh.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/adh.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/adh.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/adh.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/parens_intree.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/parens_intree.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/parens_intree.tre "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/parens_intree.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/parens_intree.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/parens_intree.tre /usr/bin/python ../../test/roundTripNCLTest.py -x ../../example/normalizer/NEXUSnormalizer ../../test/funkyValidIn ../../test/funkyValidOut "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/libncl-2.1.21+git20180827.c71b264/test/funkyValidIn/choke.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/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 ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/funkyValidIn/choke.tre "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/libncl-2.1.21+git20180827.c71b264/test/funkyValidOut/choke.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/funkyValidOut/choke.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/funkyValidOut/choke.tre /usr/bin/python ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy ] Executing storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy ] Executing storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylip_emboss.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylip_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylip_emboss.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylip_emboss.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylip_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylip_emboss.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aafasta_twoprot.fas" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aafasta_twoprot.fas ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aafasta_twoprot.fas "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aafasta_twoprot.fas" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aafasta_twoprot.fas ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aafasta_twoprot.fas "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot_undec.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot_undec.aln "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot_undec.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot_undec.aln "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln /usr/bin/python ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/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/python ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer /nonexistent/first-build/.ncl_round_triprc does not exist. Test stepped skipped. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' Making check in ot-subtree make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' Making check in ot-tree-inspect make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' Making check in outdeg1count make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' Making check in patristic make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/patristic' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/patristic' Making check in phylobaseinterface make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/phylobaseinterface' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/phylobaseinterface' Making check in polytomy-count make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/polytomy-count' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/polytomy-count' Making check in splitsinfile make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/splitsinfile' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/splitsinfile' Making check in subsetter make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/subsetter' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/subsetter' Making check in translate make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/translate' make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/translate' /usr/bin/python ../../test/roundTripNCLTest.py -o ../../example/translate/NEXUStranslate ../../test/TranslateIn ../../test/TranslateOut "/build/libncl-2.1.21+git20180827.c71b264/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/TranslateIn/bglobinoof.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/TranslateIn/bglobinoof.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: CODONS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/TranslateIn/bglobinoof.nex "/build/libncl-2.1.21+git20180827.c71b264/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/TranslateIn/bglobin.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/TranslateIn/bglobin.nex make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/translate' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/translate' make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example' make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example' Making check in test make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/test' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/test' make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' make[1]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j1 install DESTDIR=/build/libncl-2.1.21\+git20180827.c71b264/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' Making install in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-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+git20180827.c71b264/debian/tmp/usr/lib/aarch64-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+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.la libtool: install: /usr/bin/install -c .libs/libncl.a /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: install: chmod 644 /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: install: ranlib /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/debian/tmp/usr/include/ncl' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' Making install in example make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example' Making install in basiccmdline make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/basiccmdline' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' Making install in check-taxo-nodes make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/checktaxonnodes /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/checktaxonnodes make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' Making install in compressor make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/compressor' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' Making install in find-unsupported-edges make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/findunsupportededges /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/findunsupportededges make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' Making install in gapcode make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/gapcode' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' Making install in nclsimplest make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/nclsimplest' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' Making install in ncltest make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/ncltest' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' Making install in normalizer make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSnormalizer /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/NEXUSnormalizer libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSvalidator /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/NEXUSvalidator libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NCLconverter /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/NCLconverter make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' Making install in ot-subtree make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/otsubtree /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/otsubtree make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' Making install in ot-tree-inspect make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/otTreeInspect /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/otTreeInspect make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' Making install in outdeg1count make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/outdeg1count /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/outdeg1count make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' Making install in patristic make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/patristic' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/patristic' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/patristic' Making install in phylobaseinterface make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/phylobaseinterface' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/phylobaseinterface' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/phylobaseinterface' Making install in polytomy-count make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/polytomy-count' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/polytomy-count' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/polytomy-count' Making install in splitsinfile make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/splitsinfile' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/splitsinfile' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/splitsinfile' Making install in subsetter make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/subsetter' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/subsetter' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/subsetter' Making install in translate make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/translate' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example/translate' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/translate' make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/example' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example' make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example' Making install in test make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/test' make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/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+git20180827.c71b264/test' make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/test' make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 nclv2.1.pc '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' make[1]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' debian/rules override_dh_install make[1]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' dh_install # bash debian/ d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/ncl/*.h" usr/include/ncl \ debian/tmp/usr/lib/*/libncl.so Library package automatic movement utility set -e install -d -m 755 debian/libncl-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libncl2/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a debian/libncl-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.la debian/libncl-dev/usr/lib/aarch64-linux-gnu || true mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so debian/libncl-dev/usr/lib/aarch64-linux-gnu mv /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/aarch64-linux-gnu mv /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/aarch64-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 make[1]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps 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-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_arm64.deb'. dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20180827.c71b264-2_arm64.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20180827.c71b264-2_arm64.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20180827.c71b264-2_arm64.deb'. dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20180827.c71b264-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libncl_2.1.21+git20180827.c71b264-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration 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/3893 and its subdirectories I: Current time: Mon Dec 6 14:18:27 -12 2021 I: pbuilder-time-stamp: 1638843507 Tue Nov 3 19:55:31 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink12-arm64.debian.net. Tue Nov 3 19:55:31 UTC 2020 I: Preparing to do remote build '2' on codethink12-arm64.debian.net. Tue Nov 3 20:03:46 UTC 2020 I: Deleting $TMPDIR on codethink12-arm64.debian.net. Tue Nov 3 20:03:47 UTC 2020 I: libncl_2.1.21+git20180827.c71b264-2_arm64.changes: Format: 1.8 Date: Thu, 07 Mar 2019 19:13:02 +0100 Source: libncl Binary: libncl-dev libncl2 libncl2-dbgsym ncl-tools ncl-tools-dbgsym Architecture: arm64 Version: 2.1.21+git20180827.c71b264-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libncl-dev - NEXUS Class Library (static lib and header files) libncl2 - NEXUS Class Library ncl-tools - tools to deal with NEXUS files Closes: 923955 Changes: libncl (2.1.21+git20180827.c71b264-2) unstable; urgency=medium . * Rebuild for new version of gcc to fix symbols Closes: #923955 * Standards-Version: 4.3.0 Checksums-Sha1: 1dfb3524d438c1f1e9412982b34d79fac37ad3c8 512732 libncl-dev_2.1.21+git20180827.c71b264-2_arm64.deb 03abcd42601e4f20da69fef6d2643ca5cf015db9 8229472 libncl2-dbgsym_2.1.21+git20180827.c71b264-2_arm64.deb f31350fd370e458ccd3c8b44a7f5bc1089471ac4 322964 libncl2_2.1.21+git20180827.c71b264-2_arm64.deb 9b279f3e791e44ca233b9f572c486eeccce8ca8a 6674 libncl_2.1.21+git20180827.c71b264-2_arm64.buildinfo 8769b4a14be9f0331d008be4c6efe8ae4c812667 6914784 ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_arm64.deb b8c634490502d2975785deaff2796d8eb38ca4a8 180128 ncl-tools_2.1.21+git20180827.c71b264-2_arm64.deb Checksums-Sha256: 08ab38d3179d4a223951aaa6e91ae796f9afab2f67c08eda16ce25bd73132e7e 512732 libncl-dev_2.1.21+git20180827.c71b264-2_arm64.deb 3d4d2340206d2c21c9936dd9ae7da4c629279f8d1d5b267a88908e7692eef795 8229472 libncl2-dbgsym_2.1.21+git20180827.c71b264-2_arm64.deb ce72aded6642a5868e572523702adff11fd3633fbe6b300db4148941df6c6fcb 322964 libncl2_2.1.21+git20180827.c71b264-2_arm64.deb fdcff82d1738d3524fabe7db5395df563087f31e10a3b7910521999fb44527d6 6674 libncl_2.1.21+git20180827.c71b264-2_arm64.buildinfo 3e95043b1df6390642197ecb30c3fe8235ccaca1177ba80eafa36becaaa88079 6914784 ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_arm64.deb 38af8d9d42ce03ae511c0178adfb254ab24fa64aef4a17bb20786ef559fc56d5 180128 ncl-tools_2.1.21+git20180827.c71b264-2_arm64.deb Files: bd7efdf55460931247c853a6e4119e85 512732 libdevel optional libncl-dev_2.1.21+git20180827.c71b264-2_arm64.deb 1bcf252a776b7b8fef44f1964c9ab349 8229472 debug optional libncl2-dbgsym_2.1.21+git20180827.c71b264-2_arm64.deb acb58cdab1bf34541de52048d100703d 322964 libs optional libncl2_2.1.21+git20180827.c71b264-2_arm64.deb 59cb1b2991a4ba988d7be1f74b017121 6674 science optional libncl_2.1.21+git20180827.c71b264-2_arm64.buildinfo e3ba1d38725790b7fe356905a6eaed57 6914784 debug optional ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_arm64.deb d0d03d0bf083396b6815332edf70060e 180128 science optional ncl-tools_2.1.21+git20180827.c71b264-2_arm64.deb Tue Nov 3 20:03:51 UTC 2020 I: diffoscope 161 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.iZo1X8IeHO/libncl_2.1.21+git20180827.c71b264-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.iZo1X8IeHO/libncl_2.1.21+git20180827.c71b264-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.iZo1X8IeHO/libncl_2.1.21+git20180827.c71b264-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.iZo1X8IeHO/b1/libncl_2.1.21+git20180827.c71b264-2_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.iZo1X8IeHO/b2/libncl_2.1.21+git20180827.c71b264-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.514s) 0.514s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.181s) 0.180s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Nov 3 20:03:53 UTC 2020 I: diffoscope 161 found no differences in the changes files, and a .buildinfo file also exists. Tue Nov 3 20:03:53 UTC 2020 I: libncl from buster built successfully and reproducibly on arm64. Tue Nov 3 20:03:56 UTC 2020 I: Submitting .buildinfo files to external archives: Tue Nov 3 20:03:56 UTC 2020 I: Submitting 8.0K b1/libncl_2.1.21+git20180827.c71b264-2_arm64.buildinfo.asc Tue Nov 3 20:03:57 UTC 2020 I: Submitting 8.0K b2/libncl_2.1.21+git20180827.c71b264-2_arm64.buildinfo.asc Tue Nov 3 20:03:58 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Nov 3 20:03:58 UTC 2020 I: Done submitting .buildinfo files. Tue Nov 3 20:03:58 UTC 2020 I: Removing signed libncl_2.1.21+git20180827.c71b264-2_arm64.buildinfo.asc files: removed './b1/libncl_2.1.21+git20180827.c71b264-2_arm64.buildinfo.asc' removed './b2/libncl_2.1.21+git20180827.c71b264-2_arm64.buildinfo.asc'