Sat Mar 14 10:58:13 UTC 2020 I: starting to build libncl/buster/i386 on jenkins on '2020-03-14 10:57' Sat Mar 14 10:58:13 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_7/2870/console.log Sat Mar 14 10:58:13 UTC 2020 I: Downloading source for buster/libncl=2.1.21+git20180827.c71b264-2 --2020-03-14 10:58:13-- 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% 12.3M=0s 2020-03-14 10:58:13 (12.3 MB/s) - ‘libncl_2.1.21+git20180827.c71b264-2.dsc’ saved [2180/2180] Sat Mar 14 10:58:13 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----- Sat Mar 14 10:58:13 UTC 2020 I: Checking whether the package is not for us Sat Mar 14 10:58:13 UTC 2020 I: Starting 1st build on remote node profitbricks-build12-i386.debian.net. Sat Mar 14 10:58:13 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build12-i386.debian.net. Sat Mar 14 11:11:06 UTC 2020 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 13 22:58:16 -12 2020 I: pbuilder-time-stamp: 1584183496 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: using eatmydata during job 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 '/root/.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 -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 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 ... 19231 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 25.5 MB of archives. After unpacking 92.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 libpython2.7-minimal i386 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main i386 python2.7-minimal i386 2.7.16-2+deb10u1 [1381 kB] Get: 9 http://deb.debian.org/debian buster/main i386 python2-minimal i386 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main i386 python-minimal i386 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u2 [1538 kB] Get: 12 http://deb.debian.org/debian buster/main i386 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-2+deb10u1 [104 kB] Get: 14 http://deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libpython2.7-stdlib i386 2.7.16-2+deb10u1 [1934 kB] Get: 17 http://deb.debian.org/debian buster/main i386 python2.7 i386 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libpython2-stdlib i386 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main i386 libpython-stdlib i386 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main i386 python2 i386 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main i386 python i386 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 25 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 26 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 28 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 29 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main i386 d-shlibs all 0.84 [17.2 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 40 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 46 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 47 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Fetched 25.5 MB in 17s (1516 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:i386. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_i386.deb ... Unpacking libpython2.7-minimal:i386 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_i386.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_i386.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_i386.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:i386. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u2_i386.deb ... Unpacking libssl1.1:i386 (1.1.1d-0+deb10u2) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_i386.deb ... Unpacking libexpat1:i386 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:i386. Preparing to unpack .../14-libreadline7_7.0-5_i386.deb ... Unpacking libreadline7:i386 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:i386. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_i386.deb ... Unpacking libpython2.7-stdlib:i386 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_i386.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:i386. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_i386.deb ... Unpacking libpython2-stdlib:i386 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:i386. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_i386.deb ... Unpacking libpython-stdlib:i386 (2.7.16-1) ... Setting up libpython2.7-minimal:i386 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20696 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_i386.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20729 files and directories currently installed.) Preparing to unpack .../00-python_2.7.16-1_i386.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../03-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../06-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../07-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../08-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. 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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 i386 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=i686-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/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-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... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-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 -j10 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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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/findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' Making all in gapcode make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' 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 NEXUSgapcode-gapcode.o `test -f 'gapcode.cpp' || echo './'`gapcode.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong 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/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 nclsimplest nclsimplest.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/nclsimplest nclsimplest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' Making all in ncltest make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' 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 ncltest.o ncltest.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 ncltest ncltest.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/ncltest ncltest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' Making all in normalizer make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' 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 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-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 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 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 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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 /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/majrule splitsinfile.o splitsstructs.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/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 -j10 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/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/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/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/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/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/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/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/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/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/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/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/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-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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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" "-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" "-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" "-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" "-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" "-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" "-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.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 "/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 /usr/bin/python ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn "/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) "/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) /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/i386-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-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/i386-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-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/i386-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/i386-linux-gnu/libncl.la libtool: install: /usr/bin/install -c .libs/libncl.a /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu/libncl.a libtool: install: chmod 644 /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu/libncl.a libtool: install: ranlib /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-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/i386-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/i386-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/i386-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/i386-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/i386-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/i386-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/i386-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/i386-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/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 nclv2.1.pc '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-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/i386-linux-gnu install -d -m 755 debian/libncl2/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libncl.a debian/libncl-dev/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libncl.la debian/libncl-dev/usr/lib/i386-linux-gnu || true mv debian/tmp/usr/lib/i386-linux-gnu/libncl.so debian/libncl-dev/usr/lib/i386-linux-gnu mv /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/i386-linux-gnu mv /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/i386-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' in '../ncl-tools_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libncl_2.1.21+git20180827.c71b264-2_i386.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/17966 and its subdirectories I: Current time: Fri Mar 13 23:11:05 -12 2020 I: pbuilder-time-stamp: 1584184265 Sat Mar 14 11:11:06 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build16-i386.debian.net. Sat Mar 14 11:11:06 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build16-i386.debian.net. Sat Mar 14 11:13:55 UTC 2020 I: Deleting $TMPDIR on profitbricks-build16-i386.debian.net. Sat Mar 14 11:13:55 UTC 2020 I: libncl_2.1.21+git20180827.c71b264-2_i386.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: i386 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: 9a0e26a1f5321656487ae80b039f3e1457023517 592368 libncl-dev_2.1.21+git20180827.c71b264-2_i386.deb 4b4ec1c9ccd4104c322409670c786ea6b44456dd 8207228 libncl2-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb 1d03bfcac4c91a905f80e8502eff8eb71710f701 408252 libncl2_2.1.21+git20180827.c71b264-2_i386.deb 7628599446e09ae54bc83dc7f53a336fb3bd4306 6645 libncl_2.1.21+git20180827.c71b264-2_i386.buildinfo 83d7f186150b5a76b711b49ad141b5bd949d71a7 6637016 ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb bc8bd86560966d27cbeefd61b0dab071a3972ebf 206648 ncl-tools_2.1.21+git20180827.c71b264-2_i386.deb Checksums-Sha256: ba6b3564e5cee74e03d32af726102d0cb59a36e9c1a9db647979d8fa5bcae27d 592368 libncl-dev_2.1.21+git20180827.c71b264-2_i386.deb ee475058dcc61299bb077c42e552550b5d05efc0560bd477f6cddda749508cd4 8207228 libncl2-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb 27ca304f67ba63d483c3cfaccfa017d7f9d9d264786533b304350ef2abf9acfd 408252 libncl2_2.1.21+git20180827.c71b264-2_i386.deb 8274d0cca84d9f870c21bbf0e86f4b9b9e315a393227b68e68450afe5564a545 6645 libncl_2.1.21+git20180827.c71b264-2_i386.buildinfo 913eaea951e83be5c2ea8aa5036b8c4116573a74c419653f06c520ded1dfe3b5 6637016 ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb 691ca2b26c21896934a40901872b4b81f7dc46498dd62ed5aeb71b1c2c8f57fa 206648 ncl-tools_2.1.21+git20180827.c71b264-2_i386.deb Files: 6fa644c7b99f2094315eba6ad97450ab 592368 libdevel optional libncl-dev_2.1.21+git20180827.c71b264-2_i386.deb 155c4a7389f69c35ad8958ca898db401 8207228 debug optional libncl2-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb 1f1d7928b28ba2c8165e47a6c8885dbb 408252 libs optional libncl2_2.1.21+git20180827.c71b264-2_i386.deb 10c223164d93d5962d16c35d44d43f32 6645 science optional libncl_2.1.21+git20180827.c71b264-2_i386.buildinfo 97beb394ee38b4c4a87ab2dfd69e6a9c 6637016 debug optional ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb 87f2d6f7f9b5ee9aebc67f19046e5111 206648 science optional ncl-tools_2.1.21+git20180827.c71b264-2_i386.deb Sat Mar 14 11:13:57 UTC 2020 I: diffoscope 137 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.IJwFdWeWFs/libncl_2.1.21+git20180827.c71b264-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.IJwFdWeWFs/libncl_2.1.21+git20180827.c71b264-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.IJwFdWeWFs/libncl_2.1.21+git20180827.c71b264-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.IJwFdWeWFs/b1/libncl_2.1.21+git20180827.c71b264-2_i386.changes /srv/reproducible-results/rbuild-debian/tmp.IJwFdWeWFs/b2/libncl_2.1.21+git20180827.c71b264-2_i386.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: 0.284s) 0.284s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.090s) 0.090s 10 calls diffoscope.comparators.binary.FilesystemFile Sat Mar 14 11:13:59 UTC 2020 I: diffoscope 137 found no differences in the changes files, and a .buildinfo file also exists. Sat Mar 14 11:13:59 UTC 2020 I: libncl from buster built successfully and reproducibly on i386. Sat Mar 14 11:14:00 UTC 2020 I: Submitting .buildinfo files to external archives: Sat Mar 14 11:14:00 UTC 2020 I: Submitting 8.0K b1/libncl_2.1.21+git20180827.c71b264-2_i386.buildinfo.asc Sat Mar 14 11:14:02 UTC 2020 I: Submitting 8.0K b2/libncl_2.1.21+git20180827.c71b264-2_i386.buildinfo.asc Sat Mar 14 11:14:04 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Mar 14 11:14:04 UTC 2020 I: Done submitting .buildinfo files. Sat Mar 14 11:14:04 UTC 2020 I: Removing signed libncl_2.1.21+git20180827.c71b264-2_i386.buildinfo.asc files: removed './b1/libncl_2.1.21+git20180827.c71b264-2_i386.buildinfo.asc' removed './b2/libncl_2.1.21+git20180827.c71b264-2_i386.buildinfo.asc'