I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 17 07:34:07 +14 2021 I: pbuilder-time-stamp: 1618594447 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 Fri Mar 8 08:17:52 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libncl_2.1.21+git20180827.c71b264-2.dsc dpkg-source: info: extracting libncl in libncl-2.1.21+git20180827.c71b264 dpkg-source: info: unpacking libncl_2.1.21+git20180827.c71b264.orig.tar.xz dpkg-source: info: unpacking libncl_2.1.21+git20180827.c71b264-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_rpath_issue.patch dpkg-source: info: applying set_soname_version.patch dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/58725/tmp/hooks/D01_modify_environment starting disorder-fs debug: Running on profitbricks-build16-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/58725/tmp/hooks/D01_modify_environment finished -> 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 0s (84.3 MB/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. Preparing to unpack .../09-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../10-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../11-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../12-d-shlibs_0.84_all.deb ... Unpacking d-shlibs (0.84) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../16-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../17-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../18-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../19-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../20-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../21-libicu63_63.1-6_i386.deb ... Unpacking libicu63:i386 (63.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../22-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../23-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../24-libncurses6_6.1+20181013-2+deb10u2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-9_i386.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Setting up libexpat1:i386 (2.2.6-2+deb10u1) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up mime-support (3.62) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:i386 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:i386 (1.1.1d-0+deb10u2) ... Setting up libmagic1:i386 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:i386 (63.1-6) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up d-shlibs (0.84) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:i386 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:i386 (2.7.16-2+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:i386 (2.7.16-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:i386 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/libncl-2.1.21+git20180827.c71b264/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 '2222' is supported by ustar format... yes checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... 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 -j18 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/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsassumptionsblock.lo nxsassumptionsblock.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsblock.lo nxsblock.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscharactersblock.lo nxscharactersblock.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscxxdiscretematrix.lo nxscxxdiscretematrix.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdatablock.lo nxsdatablock.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdistancesblock.lo nxsdistancesblock.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsexception.lo nxsexception.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsmultiformat.lo nxsmultiformat.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxspublicblocks.lo nxspublicblocks.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsreader.lo nxsreader.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxssetreader.lo nxssetreader.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsstring.lo nxsstring.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstoken.lo nxstoken.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -fPIC -DPIC -o .libs/nxscxxdiscretematrix.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -fPIC -DPIC -o .libs/nxsblock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsassumptionsblock.cpp -fPIC -DPIC -o .libs/nxsassumptionsblock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -fPIC -DPIC -o .libs/nxsmultiformat.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -fPIC -DPIC -o .libs/nxsstring.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -fPIC -DPIC -o .libs/nxstoken.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -o nxstaxaassociationblock.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -o nxsunalignedblock.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 libtool: 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 -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 /bin/sh ../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 -version-info 2:0:0 -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/i386-linux-gnu nxsassumptionsblock.lo nxsblock.lo nxscharactersblock.lo nxscxxdiscretematrix.lo nxsdatablock.lo nxsdistancesblock.lo nxsexception.lo nxsmultiformat.lo nxspublicblocks.lo nxsreader.lo nxssetreader.lo nxsstring.lo nxstaxablock.lo nxstaxaassociationblock.lo nxstoken.lo nxstreesblock.lo nxsunalignedblock.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/8/crtbeginS.o .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxscxxdiscretematrix.o .libs/nxsdatablock.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsmultiformat.o .libs/nxspublicblocks.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstaxaassociationblock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -L/usr/lib/gcc/i686-linux-gnu/8 -L/usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/8/crtendS.o /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -O3 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libncl.so.2" && ln -s "libncl.so.2.0.0" "libncl.so.2") libtool: link: (cd ".libs" && rm -f "libncl.so" && ln -s "libncl.so.2.0.0" "libncl.so") libtool: link: ar cru .libs/libncl.a nxsassumptionsblock.o nxsblock.o nxscharactersblock.o nxscxxdiscretematrix.o nxsdatablock.o nxsdistancesblock.o nxsexception.o nxsmultiformat.o nxspublicblocks.o nxsreader.o nxssetreader.o nxsstring.o nxstaxablock.o nxstaxaassociationblock.o nxstoken.o nxstreesblock.o nxsunalignedblock.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libncl.a libtool: link: ( cd ".libs" && rm -f "libncl.la" && ln -s "../libncl.la" "libncl.la" ) make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' Making all in example make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example' Making all in basiccmdline make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' 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 basiccmdline.o basiccmdline.cpp /bin/sh ../../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 basiccmdline basiccmdline.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/basiccmdline basiccmdline.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' Making all in check-taxo-nodes make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' 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 checktaxonnodes-checktaxonnodes.o `test -f 'checktaxonnodes.cpp' || echo './'`checktaxonnodes.cpp /bin/sh ../../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 checktaxonnodes checktaxonnodes-checktaxonnodes.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/checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' Making all in compressor make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' 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 NEXUSCharacterCompressor-compressor.o `test -f 'compressor.cpp' || echo './'`compressor.cpp /bin/sh ../../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 NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.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/NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' Making all in find-unsupported-edges make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' 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 findunsupportededges-findunsupportededges.o `test -f 'findunsupportededges.cpp' || echo './'`findunsupportededges.cpp /bin/sh ../../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 findunsupportededges findunsupportededges-findunsupportededges.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/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/sh ../../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 NEXUSgapcode NEXUSgapcode-gapcode.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/NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' Making all in nclsimplest make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' g++ -DHAVE_CONFIG_H -I. -I../.. -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -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 nclsimplest.o nclsimplest.cpp /bin/sh ../../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/sh ../../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 -ffast-math -c -o normalizer.o normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_VALIDATE_NEXUS -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 NEXUSvalidator-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -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 NCLconverter-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -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 NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -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 NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -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 NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -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 NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -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 NEX_us2ml-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DMULTIFILE_NEXUS_READER -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 NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp /bin/sh ../../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 NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la /bin/sh ../../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 NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la /bin/sh ../../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 NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.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/NEXUSvalidator NEXUSvalidator-normalizer.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/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so /bin/sh ../../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 NEXUSnormalizer normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' Making all in ot-subtree make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otsubtree-otsubtree.o `test -f 'otsubtree.cpp' || echo './'`otsubtree.cpp /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' Making all in ot-tree-inspect make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otTreeInspect-ot_tree_inspect.o `test -f 'ot_tree_inspect.cpp' || echo './'`ot_tree_inspect.cpp /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' Making all in outdeg1count make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o outdeg1count-outdeg1count.o `test -f 'outdeg1count.cpp' || echo './'`outdeg1count.cpp /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' Making all in patristic make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/patristic' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o patristic.o patristic.cpp /bin/sh ../../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/sh ../../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/sh ../../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/sh ../../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 /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-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/majrule splitsinfile.o 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/sh ../../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/sh ../../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 -j18 check VERBOSE=1 make[1]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' Making check in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' Making check in example make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example' Making check in basiccmdline make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' Making check in check-taxo-nodes make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' Making check in compressor make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' Making check in find-unsupported-edges make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' Making check in gapcode make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' Making check in nclsimplest make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' Making check in ncltest make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' /usr/bin/python ../../test/roundTripNCLTest.py ../../example/ncltest/ncltest ../../test/OldValidIn ../../test/OldValidOut "/build/libncl-2.1.21+git20180827.c71b264/example/ncltest/ncltest" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/OldValidIn/m.nex" [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/ncltest/ncltest succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/OldValidIn/m.nex "/build/libncl-2.1.21+git20180827.c71b264/example/ncltest/ncltest" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/OldValidOut/m.nex" [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/ncltest/ncltest succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/OldValidOut/m.nex make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' Making check in normalizer make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' /usr/bin/python ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/characters.nex ../../test/data "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/data/characters.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/data/characters.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/data/characters.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/data/characters.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/data/characters.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/data/characters.nex /usr/bin/python ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/sample.tre ../../test/data "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/data/sample.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/data/sample.tre ] Executing storing read block: PAUP storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/data/sample.tre "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/data/sample.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/data/sample.tre ] Executing storing read block: PAUP storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/data/sample.tre /usr/bin/python ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/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/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/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/avian_ovomucoids.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex ] Executing storing read block: TAXA storing read block: TAXA storing read block: TAXAASSOCIATION ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex ] Executing storing read block: TAXA storing read block: TAXA storing read block: TAXAASSOCIATION ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/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/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/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/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/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/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/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/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/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/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/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/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/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/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/anolis.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/adh.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/adh.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/adh.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/adh.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/adh.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/adh.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/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/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/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/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/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/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/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/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" "-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" "-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" "-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" "-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" "-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" "-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" "-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" "-faafasta" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aafasta_twoprot.fas" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aafasta_twoprot.fas ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aafasta_twoprot.fas "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aafasta_twoprot.fas" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aafasta_twoprot.fas ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aafasta_twoprot.fas "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot_undec.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot_undec.aln ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot_undec.aln "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot_undec.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot_undec.aln ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot_undec.aln "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln /usr/bin/python ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy ] Executing Error: Illegal state code "q" found when reading site 2 for taxon grylioMVZ175945 at line 12, column (approximately) 28 (and file position 20065) "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/aarelaxedphylip_rana.phy ] Executing Error: Sequence longer than 1976 found for taxon temporariaDMH84R1. The character "o" was found, and will be ignored. If the file position of this error corresponds to sequences for the next taxon in the matrix, then that is an indication that the sequences for taxon temporariaDMH84R1 are too short. at line 3, column (approximately) 2 (and file position 2011) /usr/bin/python ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer /nonexistent/second-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/sh ../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/sh ../../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/sh ../../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/sh ../../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/sh ../../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/sh ../../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/sh ../../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 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_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 '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: user script /srv/workspace/pbuilder/58725/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/58725/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/58725 and its subdirectories I: Current time: Sat Apr 17 07:36:54 +14 2021 I: pbuilder-time-stamp: 1618594614