I: pbuilder: network access will be disabled during build
I: Current time: Wed Aug 11 07:54:49 -12 2021
I: pbuilder-time-stamp: 1628711689
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [libncl_2.1.21+git20190531.feceb81-3.dsc]
I: copying [./libncl_2.1.21+git20190531.feceb81.orig.tar.xz]
I: copying [./libncl_2.1.21+git20190531.feceb81-3.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.JtJ75LVk/trustedkeys.kbx': General error
gpgv: Signature made Thu Jul 23 01:04:01 2020 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libncl_2.1.21+git20190531.feceb81-3.dsc
dpkg-source: info: extracting libncl in libncl-2.1.21+git20190531.feceb81
dpkg-source: info: unpacking libncl_2.1.21+git20190531.feceb81.orig.tar.xz
dpkg-source: info: unpacking libncl_2.1.21+git20190531.feceb81-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_rpath_issue.patch
dpkg-source: info: applying set_soname_version.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying 2to3.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/6296/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3'
DISTRIBUTION=''
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='52715cf0027f44b5964045404b56be34'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='6296'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Vou8RLBIzA/pbuilderrc_wsss --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Vou8RLBIzA/b1 --logfile b1/build.log libncl_2.1.21+git20190531.feceb81-3.dsc'
SUDO_GID='114'
SUDO_UID='108'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:8000/'
I: uname -a
Linux jtx1c 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux
I: ls -l /bin
total 3580
-rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash
-rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2
-rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep
-rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2
-rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore
-rwxr-xr-x 1 root root 26668 Sep 22 2020 cat
-rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp
-rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod
-rwxr-xr-x 1 root root 43112 Sep 22 2020 chown
-rwxr-xr-x 1 root root 92616 Sep 22 2020 cp
-rwxr-xr-x 1 root root 75524 Dec 10 2020 dash
-rwxr-xr-x 1 root root 75880 Sep 22 2020 date
-rwxr-xr-x 1 root root 55436 Sep 22 2020 dd
-rwxr-xr-x 1 root root 59912 Sep 22 2020 df
-rwxr-xr-x 1 root root 96764 Sep 22 2020 dir
-rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg
lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname
-rwxr-xr-x 1 root root 22508 Sep 22 2020 echo
-rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
-rwxr-xr-x 1 root root 22496 Sep 22 2020 false
-rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
-rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt
-rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount
-rwxr-xr-x 1 root root 124508 Nov 9 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip
-rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe
-rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip
-rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname
-rwxr-xr-x 1 root root 43180 Sep 22 2020 ln
-rwxr-xr-x 1 root root 35068 Feb 7 2020 login
-rwxr-xr-x 1 root root 96764 Sep 22 2020 ls
-rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk
-rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir
-rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod
-rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp
-rwxr-xr-x 1 root root 34408 Jul 28 07:09 more
-rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount
-rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint
-rwxr-xr-x 1 root root 88524 Sep 22 2020 mv
lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd
lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash
-rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink
-rwxr-xr-x 1 root root 43104 Sep 22 2020 rm
-rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir
-rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts
-rwxr-xr-x 1 root root 76012 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Aug 9 21:25 sh -> dash
-rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep
-rwxr-xr-x 1 root root 55360 Sep 22 2020 stty
-rwsr-xr-x 1 root root 46704 Jul 28 07:09 su
-rwxr-xr-x 1 root root 22532 Sep 22 2020 sync
-rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar
-rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile
-rwxr-xr-x 1 root root 67696 Sep 22 2020 touch
-rwxr-xr-x 1 root root 22496 Sep 22 2020 true
-rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount
-rwxr-xr-x 1 root root 22520 Sep 22 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress
-rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir
-rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl
lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat
-rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp
-rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff
-rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep
-rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce
-rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep
-rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless
-rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore
-rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew
I: user script /srv/workspace/pbuilder/6296/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), d-shlibs, python3
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19398 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on d-shlibs; however:
Package d-shlibs is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.7 MB of archives. After unpacking 80.9 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB]
Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB]
Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB]
Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB]
Get: 6 http://deb.debian.org/debian bullseye/main armhf libpython3.9-minimal armhf 3.9.2-1 [790 kB]
Get: 7 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB]
Get: 8 http://deb.debian.org/debian bullseye/main armhf python3.9-minimal armhf 3.9.2-1 [1630 kB]
Get: 9 http://deb.debian.org/debian bullseye/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get: 10 http://deb.debian.org/debian bullseye/main armhf media-types all 4.0.0 [30.3 kB]
Get: 11 http://deb.debian.org/debian bullseye/main armhf libmpdec3 armhf 2.5.1-1 [74.9 kB]
Get: 12 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB]
Get: 13 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB]
Get: 14 http://deb.debian.org/debian bullseye/main armhf libpython3.9-stdlib armhf 3.9.2-1 [1608 kB]
Get: 15 http://deb.debian.org/debian bullseye/main armhf python3.9 armhf 3.9.2-1 [466 kB]
Get: 16 http://deb.debian.org/debian bullseye/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get: 17 http://deb.debian.org/debian bullseye/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get: 18 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB]
Get: 19 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get: 20 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get: 21 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB]
Get: 22 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB]
Get: 23 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB]
Get: 24 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB]
Get: 25 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB]
Get: 26 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 27 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB]
Get: 28 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB]
Get: 29 http://deb.debian.org/debian bullseye/main armhf d-shlibs all 0.98 [17.9 kB]
Get: 30 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get: 31 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB]
Get: 32 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 33 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 34 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get: 35 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get: 36 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get: 37 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB]
Get: 38 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB]
Get: 39 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB]
Get: 40 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB]
Get: 41 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB]
Get: 42 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 43 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 44 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB]
Fetched 22.7 MB in 2s (10.6 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
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Preparing to unpack .../0-bsdextrautils_2.36.1-8_armhf.deb ...
Unpacking bsdextrautils (2.36.1-8) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../2-groff-base_1.22.4-6_armhf.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../3-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
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Preparing to unpack .../4-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
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Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.2-1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../6-libexpat1_2.2.10-2_armhf.deb ...
Unpacking libexpat1:armhf (2.2.10-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../7-python3.9-minimal_3.9.2-1_armhf.deb ...
Unpacking python3.9-minimal (3.9.2-1) ...
Setting up libpython3.9-minimal:armhf (3.9.2-1) ...
Setting up libexpat1:armhf (2.2.10-2) ...
Setting up python3.9-minimal (3.9.2-1) ...
Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.9.2-3) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package libmpdec3:armhf.
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Unpacking libmpdec3:armhf (2.5.1-1) ...
Selecting previously unselected package readline-common.
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Unpacking readline-common (8.1-1) ...
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Unpacking python3.9 (3.9.2-1) ...
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Unpacking python3 (3.9.2-3) ...
Selecting previously unselected package sensible-utils.
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Unpacking sensible-utils (0.0.14) ...
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I: Building the package
I: Running cd /build/libncl-2.1.21+git20190531.feceb81/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libncl_2.1.21+git20190531.feceb81-3_source.changes
dpkg-buildpackage: info: source package libncl
dpkg-buildpackage: info: source version 2.1.21+git20190531.feceb81-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
dh_clean
find . -name ".roundTripNCL*" -delete
make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
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libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'.
libtoolize: copying file 'config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'.
libtoolize: copying file 'config/libtool.m4'
libtoolize: copying file 'config/ltoptions.m4'
libtoolize: copying file 'config/ltsugar.m4'
libtoolize: copying file 'config/ltversion.m4'
libtoolize: copying file 'config/lt~obsolete.m4'
configure.ac:28: installing 'config/compile'
configure.ac:21: installing 'config/missing'
example/basiccmdline/Makefile.am: installing 'config/depcomp'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
dh_auto_configure -- --with-constfuncs=yes
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-constfuncs=yes
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checking how to hardcode library paths into programs... immediate
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checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
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checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating example/Makefile
config.status: creating example/basiccmdline/Makefile
config.status: creating example/check-taxo-nodes/Makefile
config.status: creating example/compressor/Makefile
config.status: creating example/find-unsupported-edges/Makefile
config.status: creating example/gapcode/Makefile
config.status: creating example/ot-subtree/Makefile
config.status: creating example/ot-tree-inspect/Makefile
config.status: creating example/nclsimplest/Makefile
config.status: creating example/ncltest/Makefile
config.status: creating example/normalizer/Makefile
config.status: creating example/patristic/Makefile
config.status: creating example/phylobaseinterface/Makefile
config.status: creating example/polytomy-count/Makefile
config.status: creating example/outdeg1count/Makefile
config.status: creating example/splitsinfile/Makefile
config.status: creating example/subsetter/Makefile
config.status: creating example/translate/Makefile
config.status: creating ncl/Makefile
config.status: creating test/Makefile
config.status: creating nclv2.1.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
dh_auto_build
make -j3
make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
make all-recursive
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
Making all in ncl
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl'
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsassumptionsblock.lo nxsassumptionsblock.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsblock.lo nxsblock.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscharactersblock.lo nxscharactersblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscxxdiscretematrix.lo nxscxxdiscretematrix.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -fPIC -DPIC -o .libs/nxscxxdiscretematrix.o
In file included from /usr/include/c++/10/vector:72,
from ../ncl/nxscxxdiscretematrix.h:25,
from nxscxxdiscretematrix.cpp:20:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const NxsCharacterPattern&}; _Tp = NxsCharacterPattern; _Alloc = std::allocator<NxsCharacterPattern>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NxsCharacterPattern>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../ncl/nxscxxdiscretematrix.h:25,
from nxscxxdiscretematrix.cpp:20:
/usr/include/c++/10/bits/stl_vector.h: In function 'void NxsConsumePatternSetToPatternVector(std::set<NxsCharacterPattern>&, std::vector<NxsCharacterPattern>&, const std::vector<const NxsCharacterPattern*>*, std::vector<int>*, std::vector<std::set<unsigned int> >*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NxsCharacterPattern*, std::vector<NxsCharacterPattern> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../ncl/nxsdefs.h:24,
from ../ncl/nxscxxdiscretematrix.h:26,
from nxscxxdiscretematrix.cpp:20:
/usr/include/c++/10/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity<NxsCharacterPattern>; _Compare = std::less<NxsCharacterPattern>; _Alloc = std::allocator<NxsCharacterPattern>]':
/usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type 'std::_Rb_tree<NxsCharacterPattern, NxsCharacterPattern, std::_Identity<NxsCharacterPattern>, std::less<NxsCharacterPattern>, std::allocator<NxsCharacterPattern> >::const_iterator' changed in GCC 7.1
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1
In file included from /usr/include/c++/10/vector:72,
from ../ncl/nxsdefs.h:23,
from ../ncl/nxscharactersblock.h:27,
from nxscharactersblock.cpp:26:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../ncl/nxsdefs.h:23,
from ../ncl/nxscharactersblock.h:27,
from nxscharactersblock.cpp:26:
/usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector<double> NxsTransformationManager::GetDoubleWeights(const string&) const':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../ncl/nxsdefs.h:23,
from ../ncl/nxscharactersblock.h:27,
from nxscharactersblock.cpp:26:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdatablock.lo nxsdatablock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o
In file included from /usr/include/c++/10/vector:67,
from ../ncl/nxsdefs.h:23,
from ../ncl/nxscharactersblock.h:27,
from nxscharactersblock.cpp:26:
/usr/include/c++/10/bits/stl_vector.h: In member function 'bool NxsCharactersBlock::HandleNextContinuousState(NxsToken&, unsigned int, unsigned int, NxsCharactersBlock::ContinuousCharRow&, const NxsString&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdistancesblock.lo nxsdistancesblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsexception.lo nxsexception.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsmultiformat.lo nxsmultiformat.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -fPIC -DPIC -o .libs/nxsmultiformat.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxspublicblocks.lo nxspublicblocks.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsreader.lo nxsreader.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxssetreader.lo nxssetreader.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsstring.lo nxsstring.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -o nxstaxaassociationblock.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstoken.lo nxstoken.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -fPIC -DPIC -o .libs/nxstoken.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o
In file included from /usr/include/c++/10/vector:72,
from ../ncl/nxsdefs.h:23,
from ../ncl/nxsstring.h:29,
from ../ncl/nxsexception.h:23,
from ../ncl/nxstoken.h:23,
from nxstoken.cpp:22:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ProcessedNxsToken}; _Tp = ProcessedNxsToken; _Alloc = std::allocator<ProcessedNxsToken>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ProcessedNxsToken>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static std::vector<ProcessedNxsToken> NxsToken::Tokenize(const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void NxsToken::ProcessAsCommand(ProcessedNxsCommand*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../ncl/nxsdefs.h:24,
from ../ncl/nxstreesblock.h:24,
from nxstreesblock.cpp:23:
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const unsigned int&>, std::tuple<>}; _Key = unsigned int; _Val = std::pair<const unsigned int, double>; _KeyOfValue = std::_Select1st<std::pair<const unsigned int, double> >; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, double> >]':
/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o
In file included from /usr/include/c++/10/map:61,
from ../ncl/nxsdefs.h:24,
from ../ncl/nxstreesblock.h:24,
from nxstreesblock.cpp:23:
/usr/include/c++/10/bits/stl_map.h: In member function 'std::vector<std::vector<double> > NxsSimpleTree::GetDblPathDistances(bool) const':
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../ncl/nxsdefs.h:23,
from ../ncl/nxstreesblock.h:24,
from nxstreesblock.cpp:23:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {NxsFullTreeDescription}; _Tp = NxsFullTreeDescription; _Alloc = std::allocator<NxsFullTreeDescription>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NxsFullTreeDescription>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {NxsFullTreeDescription}; _Tp = NxsFullTreeDescription; _Alloc = std::allocator<NxsFullTreeDescription>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NxsFullTreeDescription*, std::vector<NxsFullTreeDescription> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void NxsTreesBlock::ReadPhylipTreeFile(NxsToken&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NxsFullTreeDescription*, std::vector<NxsFullTreeDescription> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1
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libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/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/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/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
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libtool: link: ranlib .libs/libncl.a
libtool: link: ( cd ".libs" && rm -f "libncl.la" && ln -s "../libncl.la" "libncl.la" )
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g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o basiccmdline.o basiccmdline.cpp
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/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la
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g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o findunsupportededges-findunsupportededges.o `test -f 'findunsupportededges.cpp' || echo './'`findunsupportededges.cpp
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g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSgapcode-gapcode.o `test -f 'gapcode.cpp' || echo './'`gapcode.cpp
In file included from /usr/include/c++/10/vector:72,
from ../../ncl/ncl.h:60,
from gapcode.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../../ncl/ncl.h:60,
from gapcode.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void writeCharactersAsGapped(std::ostream&, NxsCharactersBlock*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la
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/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la
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g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o 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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp
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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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp
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/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la
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/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
Making all in ot-subtree
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otsubtree-otsubtree.o `test -f 'otsubtree.cpp' || echo './'`otsubtree.cpp
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree'
Making all in ot-tree-inspect
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otTreeInspect-ot_tree_inspect.o `test -f 'ot_tree_inspect.cpp' || echo './'`ot_tree_inspect.cpp
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect'
Making all in outdeg1count
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o outdeg1count-outdeg1count.o `test -f 'outdeg1count.cpp' || echo './'`outdeg1count.cpp
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count'
Making all in patristic
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o patristic.o patristic.cpp
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic'
Making all in phylobaseinterface
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLInterface.o NCLInterface.cpp
In file included from /usr/include/c++/10/vector:72,
from ../../ncl/ncl.h:60,
from NCLInterface.cpp:24:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void BASICCMDLINE::AppendRContent(NxsString&, NxsDistancesBlock&) const':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface'
Making all in polytomy-count
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o polytomycount-polytomy_count.o `test -f 'polytomy_count.cpp' || echo './'`polytomy_count.cpp
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count'
Making all in splitsinfile
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStosplits-splitsinfile.o `test -f 'splitsinfile.cpp' || echo './'`splitsinfile.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStosplits-splitsstructs.o `test -f 'splitsstructs.cpp' || echo './'`splitsstructs.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsinfile.o splitsinfile.cpp
In file included from /usr/include/c++/10/vector:72,
from splitsstructs.h:3,
from splitsstructs.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/map:60,
from ../../ncl/nxsdefs.h:24,
from splitsstructs.h:8,
from splitsstructs.cpp:1:
/usr/include/c++/10/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = Split; _Val = std::pair<const Split, SplitInfo>; _KeyOfValue = std::_Select1st<std::pair<const Split, SplitInfo> >; _Compare = std::less<Split>; _Alloc = std::allocator<std::pair<const Split, SplitInfo> >]':
/usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type 'std::_Rb_tree<Split, std::pair<const Split, SplitInfo>, std::_Select1st<std::pair<const Split, SplitInfo> >, std::less<Split>, std::allocator<std::pair<const Split, SplitInfo> > >::const_iterator' changed in GCC 7.1
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from splitsstructs.h:3,
from splitsstructs.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void TreesToSplits::recordSplit(const Split&, const NxsSimpleNode*, TreesToSplits::SplitsMap&, unsigned int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from splitsstructs.h:3,
from splitsstructs.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function 'void TreesToSplits::recordTreeToSplitsMap(const NxsFullTreeDescription&, TreesToSplits::SplitsMap&, unsigned int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so
In file included from /usr/include/c++/10/vector:72,
from splitsstructs.h:3,
from splitsstructs.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/map:60,
from ../../ncl/nxsdefs.h:24,
from splitsstructs.h:8,
from splitsstructs.cpp:1:
/usr/include/c++/10/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = Split; _Val = std::pair<const Split, SplitInfo>; _KeyOfValue = std::_Select1st<std::pair<const Split, SplitInfo> >; _Compare = std::less<Split>; _Alloc = std::allocator<std::pair<const Split, SplitInfo> >]':
/usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type 'std::_Rb_tree<Split, std::pair<const Split, SplitInfo>, std::_Select1st<std::pair<const Split, SplitInfo> >, std::less<Split>, std::allocator<std::pair<const Split, SplitInfo> > >::const_iterator' changed in GCC 7.1
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from splitsstructs.h:3,
from splitsstructs.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void TreesToSplits::recordSplit(const Split&, const NxsSimpleNode*, TreesToSplits::SplitsMap&, unsigned int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from splitsstructs.h:3,
from splitsstructs.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function 'void TreesToSplits::recordTreeToSplitsMap(const NxsFullTreeDescription&, TreesToSplits::SplitsMap&, unsigned int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile'
Making all in subsetter
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSsubsetter-subsetter.o `test -f 'subsetter.cpp' || echo './'`subsetter.cpp
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter'
Making all in translate
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStranslate-translateNuc.o `test -f 'translateNuc.cpp' || echo './'`translateNuc.cpp
In file included from /usr/include/c++/10/vector:72,
from ../../ncl/ncl.h:60,
from translateNuc.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../../ncl/ncl.h:60,
from translateNuc.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void writeCharactersAsGapped(std::ostream&, NxsCharactersBlock*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example'
Making all in test
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/test'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/test'
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
dh_auto_test
make -j3 check VERBOSE=1
make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
Making check in ncl
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/ncl'
Making check in example
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example'
Making check in basiccmdline
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline'
Making check in check-taxo-nodes
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes'
Making check in compressor
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor'
Making check in find-unsupported-edges
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges'
Making check in gapcode
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode'
Making check in nclsimplest
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest'
Making check in ncltest
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest'
make check-local
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest'
/usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/ncltest/ncltest ../../test/OldValidIn ../../test/OldValidOut
"/build/libncl-2.1.21+git20190531.feceb81/example/ncltest/ncltest" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/OldValidIn/m.nex"
[Reading -s2 ]
[Reading -s2 ]
storing read block: TAXA
storing read block: CHARACTERS
storing read block: ASSUMPTIONS
/build/libncl-2.1.21+git20190531.feceb81/example/ncltest/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated
e = open(expectedOut, "rU")
/build/libncl-2.1.21+git20190531.feceb81/example/ncltest/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated
o = open(tf, "rU")
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/ncltest/ncltest succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/OldValidIn/m.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/ncltest/ncltest" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/OldValidOut/m.nex"
[Reading -s2 ]
[Reading -s2 ]
storing read block: TAXA
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/ncltest/ncltest succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/OldValidOut/m.nex
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest'
Making check in normalizer
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
make check-local
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
/usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/characters.nex ../../test/data
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/data/characters.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/data/characters.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated
e = open(expectedOut, "rU")
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated
o = open(tf, "rU")
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/data/characters.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/data/characters.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/data/characters.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/data/characters.nex
/usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/sample.tre ../../test/data
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/data/sample.tre"
[Reading /build/libncl-2.1.21+git20190531.feceb81/data/sample.tre ]
Executing
storing read block: PAUP
storing read block: TAXA
storing read block: TREES
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated
e = open(expectedOut, "rU")
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated
o = open(tf, "rU")
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/data/sample.tre
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/data/sample.tre"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/data/sample.tre ]
Executing
storing read block: PAUP
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/data/sample.tre
/usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex ]
Executing
storing read block: TAXA
storing read block: UNALIGNED
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated
e = open(expectedOut, "rU")
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated
o = open(tf, "rU")
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex ]
Executing
storing read block: TAXA
storing read block: UNALIGNED
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mac.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mac.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mac.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mac.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mac.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mac.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/characters.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/characters.nex ]
Executing
Warning:
Skipping command: blockid
at line 13, column (approximately) 11 (file position 176)
storing read block: TAXA
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/characters.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/characters.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/characters.nex ]
Executing
Warning:
Skipping command: blockid
at line 6, column (approximately) 13 (file position 183)
storing read block: TAXA
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/characters.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex ]
Executing
Warning:
A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
at line 3, column (approximately) 10 (file position 26)
storing implied block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: SETS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/associates.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/associates.nex ]
Executing
storing read block: TAXA
storing read block: TAXA
storing read block: TAXAASSOCIATION
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/associates.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/associates.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/associates.nex ]
Executing
storing read block: TAXA
storing read block: TAXA
storing read block: TAXAASSOCIATION
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/associates.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex ]
Executing
Warning:
Skipping command: blockid
at line 13, column (approximately) 11 (file position 176)
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
storing read block: SETS
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex ]
Executing
Warning:
Skipping command: blockid
at line 6, column (approximately) 13 (file position 183)
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
storing read block: SETS
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
storing read block: CODONS
Warning:
An * is ignored in a CHARSET command
at line 67, column (approximately) 46 (file position 929)
Warning:
An * is ignored in a CHARSET command
at line 68, column (approximately) 42 (file position 968)
storing read block: ASSUMPTIONS
storing read block: ASSUMPTIONS
storing read block: MESQUITECHARMODELS
storing read block: MESQUITE
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
storing read block: CODONS
storing read block: SETS
storing read block: ASSUMPTIONS
storing read block: MESQUITECHARMODELS
storing read block: MESQUITE
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/linktest.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/linktest.nex ]
Executing
Warning:
Skipping command: blockid
at line 13, column (approximately) 11 (file position 189)
storing read block: TAXA
Warning:
Skipping command: blockid
at line 27, column (approximately) 11 (file position 388)
storing read block: TAXA
storing read block: CHARACTERS
storing read block: CHARACTERS
Warning:
Skipping unknown LINK subcommand: characters
at line 61, column (approximately) 38 (file position 1551)
storing read block: TREES
Warning:
Skipping unknown LINK subcommand: characters
at line 71, column (approximately) 38 (file position 1745)
storing read block: TREES
storing implied block: ASSUMPTIONS
storing implied block: ASSUMPTIONS
storing read block: ASSUMPTIONS
Warning:
A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s).
at line 90, column (approximately) 42 (file position 2360)
storing read block: ASSUMPTIONS
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/linktest.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/linktest.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/linktest.nex ]
Executing
Warning:
Skipping command: blockid
at line 6, column (approximately) 13 (file position 168)
storing read block: TAXA
Warning:
Skipping command: blockid
at line 12, column (approximately) 13 (file position 341)
storing read block: TAXA
storing read block: CHARACTERS
storing read block: CHARACTERS
storing read block: TREES
storing read block: TREES
storing read block: SETS
storing read block: SETS
storing read block: SETS
Warning:
A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s).
at line 84, column (approximately) 20 (file position 2384)
storing read block: SETS
storing read block: SETS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/linktest.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex ]
Executing
storing read block: TAXA
storing read block: DISTANCES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex ]
Executing
storing read block: TAXA
storing read block: DISTANCES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-dos.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-dos.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-dos.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-dos.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-dos.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-dos.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: ASSUMPTIONS
storing read block: MACCLADE
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: ASSUMPTIONS
storing read block: MACCLADE
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex ]
Executing
Warning:
A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
at line 3, column (approximately) 7 (file position 26)
storing implied block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: SETS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex ]
Executing
Warning:
Skipping command: blockid
at line 13, column (approximately) 11 (file position 176)
storing read block: TAXA
storing read block: CHARACTERS
storing read block: SETS
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex ]
Executing
Warning:
Skipping command: blockid
at line 6, column (approximately) 13 (file position 183)
storing read block: TAXA
storing read block: CHARACTERS
storing read block: SETS
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex ]
Executing
Warning:
Skipping command: blockid
at line 13, column (approximately) 11 (file position 176)
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex ]
Executing
Warning:
Skipping command: blockid
at line 6, column (approximately) 13 (file position 188)
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/nhxtree.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/nhxtree.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
storing read block: CODONS
Warning:
An * is ignored in a CHARSET command
at line 67, column (approximately) 46 (file position 1014)
Warning:
An * is ignored in a CHARSET command
at line 68, column (approximately) 42 (file position 1053)
storing read block: ASSUMPTIONS
storing read block: ASSUMPTIONS
storing read block: MESQUITECHARMODELS
storing read block: MESQUITE
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/nhxtree.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/nhxtree.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/nhxtree.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
storing read block: CODONS
storing read block: SETS
storing read block: ASSUMPTIONS
storing read block: MESQUITECHARMODELS
storing read block: MESQUITE
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/nhxtree.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex ]
Executing
Warning:
A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
at line 3, column (approximately) 13 (file position 32)
storing implied block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/parens_intree.tre"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/parens_intree.tre ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/parens_intree.tre
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/parens_intree.tre"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/parens_intree.tre ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/parens_intree.tre
/usr/bin/python3 ../../test/roundTripNCLTest.py -x ../../example/normalizer/NEXUSnormalizer ../../test/funkyValidIn ../../test/funkyValidOut
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/libncl-2.1.21+git20190531.feceb81/test/funkyValidIn/choke.tre"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/funkyValidIn/choke.tre ]
Executing
Warning:
A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
at line 5, column (approximately) 6 (file position 74)
storing implied block: TAXA
storing read block: TREES
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated
e = open(expectedOut, "rU")
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated
o = open(tf, "rU")
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/funkyValidIn/choke.tre
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/libncl-2.1.21+git20190531.feceb81/test/funkyValidOut/choke.tre"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/funkyValidOut/choke.tre ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/funkyValidOut/choke.tre
/usr/bin/python3 ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated
e = open(expectedOut, "rU")
/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated
o = open(tf, "rU")
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy ]
Executing
storing implied block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_rana.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_rana.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_rana.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_rana.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_rana.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_rana.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/phyliptree_simple.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/phyliptree_simple.phy ]
Executing
storing implied block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/phyliptree_simple.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/phyliptree_simple.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/phyliptree_simple.phy ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/phyliptree_simple.phy
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot.aln"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot.aln ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot.aln
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot.aln"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot.aln ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot.aln
/usr/bin/python3 ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy ]
Executing
Error:
Illegal state code "q" found when reading site 2 for taxon grylioMVZ175945
at line 12, column (approximately) 28 (and file position 20065)
"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalInvalidIn/aarelaxedphylip_rana.phy"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalInvalidIn/aarelaxedphylip_rana.phy ]
Executing
Error:
Sequence longer than 1976 found for taxon temporariaDMH84R1. The character "o" was found, and will be ignored. If the file position of this error corresponds to sequences for the next taxon in the matrix, then that is an indication that the sequences for taxon temporariaDMH84R1 are too short.
at line 3, column (approximately) 2 (and file position 2011)
/usr/bin/python3 ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer
/build/libncl-2.1.21+git20190531.feceb81/debian/.debhelper/generated/_source/home/.ncl_round_triprc does not exist. Test stepped skipped.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
Making check in ot-subtree
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree'
Making check in ot-tree-inspect
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect'
Making check in outdeg1count
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count'
Making check in patristic
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic'
Making check in phylobaseinterface
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface'
Making check in polytomy-count
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count'
Making check in splitsinfile
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile'
Making check in subsetter
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter'
Making check in translate
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
make check-local
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
/usr/bin/python3 ../../test/roundTripNCLTest.py -o ../../example/translate/NEXUStranslate ../../test/TranslateIn ../../test/TranslateOut
"/build/libncl-2.1.21+git20190531.feceb81/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobin.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobin.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
/build/libncl-2.1.21+git20190531.feceb81/example/translate/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated
e = open(expectedOut, "rU")
/build/libncl-2.1.21+git20190531.feceb81/example/translate/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated
o = open(tf, "rU")
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobin.nex
"/build/libncl-2.1.21+git20190531.feceb81/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobinoof.nex"
[Reading /build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobinoof.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: CODONS
../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/TranslateIn/bglobinoof.nex
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example'
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example'
Making check in test
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/test'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/test'
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
make -j1 install DESTDIR=/build/libncl-2.1.21\+git20190531.feceb81/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
Making install in ncl
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl'
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl'
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.so.2.0.0
libtool: install: (cd /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libncl.so.2.0.0 libncl.so.2 || { rm -f libncl.so.2 && ln -s libncl.so.2.0.0 libncl.so.2; }; })
libtool: install: (cd /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libncl.so.2.0.0 libncl.so || { rm -f libncl.so && ln -s libncl.so.2.0.0 libncl.so; }; })
libtool: install: /usr/bin/install -c .libs/libncl.lai /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.la
libtool: install: /usr/bin/install -c .libs/libncl.a /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.a
libtool: install: chmod 644 /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.a
libtool: install: ranlib /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/include/ncl'
/usr/bin/install -c -m 644 ncl.h nxsallocatematrix.h nxsassumptionsblock.h nxsblock.cpp nxsblock.h nxscharactersblock.h nxscdiscretematrix.h nxscxxdiscretematrix.h nxsdatablock.h nxsdefs.h nxsdiscretedatum.h nxsdistancedatum.h nxsdistancesblock.h nxsexception.h nxsmultiformat.h nxspublicblocks.h nxsreader.h nxssetreader.h nxsstring.h nxstaxablock.h nxstaxaassociationblock.h nxstoken.h nxstreesblock.h nxsunalignedblock.h nxsutilcopy.h '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/include/ncl'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/ncl'
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/ncl'
Making install in example
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example'
Making install in basiccmdline
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline'
Making install in check-taxo-nodes
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes'
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/checktaxonnodes /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/checktaxonnodes
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes'
Making install in compressor
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor'
Making install in find-unsupported-edges
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges'
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/findunsupportededges /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/findunsupportededges
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges'
Making install in gapcode
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/gapcode'
Making install in nclsimplest
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest'
Making install in ncltest
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest'
Making install in normalizer
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/NEXUSnormalizer /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/NEXUSnormalizer
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/NEXUSvalidator /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/NEXUSvalidator
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/NCLconverter /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/NCLconverter
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer'
Making install in ot-subtree
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree'
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/otsubtree /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/otsubtree
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree'
Making install in ot-tree-inspect
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect'
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/otTreeInspect /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/otTreeInspect
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect'
Making install in outdeg1count
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count'
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/outdeg1count /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin/outdeg1count
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count'
Making install in patristic
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic'
Making install in phylobaseinterface
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/phylobaseinterface'
Making install in polytomy-count
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count'
Making install in splitsinfile
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/splitsinfile'
Making install in subsetter
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter'
Making install in translate
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example/translate'
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example'
make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example'
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/example'
Making install in test
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/test'
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/test'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/test'
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/test'
make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 nclv2.1.pc '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
debian/rules override_dh_install
make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81'
dh_install
d-shlibmove --commit \
--multiarch \
--devunversioned \
--movedev "debian/tmp/usr/include/ncl/*.h" usr/include/ncl \
--movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/arm-linux-gnueabihf/pkgconfig \
debian/tmp/usr/lib/*/libncl.so
Library package automatic movement utility
set -e
install -d -m 755 debian/libncl-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libncl2/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.a debian/libncl-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.la debian/libncl-dev/usr/lib/arm-linux-gnueabihf || true
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.so debian/libncl-dev/usr/lib/arm-linux-gnueabihf
mv /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.so.2 debian/libncl2/usr/lib/arm-linux-gnueabihf
mv /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.so.2.0.0 debian/libncl2/usr/lib/arm-linux-gnueabihf
PKGDEV=libncl-dev
PKGSHL=libncl2
install -d -m 755 debian/libncl-dev/usr/include/ncl
mv debian/tmp/usr/include/ncl/*.h debian/libncl-dev/usr/include/ncl
install -d -m 755 debian/libncl-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libncl-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
rm -f debian/tmp/usr/include/ncl/nxsblock.cpp
make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81'
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libncl2/usr/lib/arm-linux-gnueabihf/libncl.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/otTreeInspect contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/NCLconverter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/findunsupportededges contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/outdeg1count contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/otsubtree contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/checktaxonnodes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/NEXUSnormalizer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/NEXUSvalidator contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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 'libncl2' in '../libncl2_2.1.21+git20190531.feceb81-3_armhf.deb'.
dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20190531.feceb81-3_armhf.deb'.
dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20190531.feceb81-3_armhf.deb'.
dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20190531.feceb81-3_armhf.deb'.
dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20190531.feceb81-3_armhf.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../libncl_2.1.21+git20190531.feceb81-3_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: 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/6296 and its subdirectories
I: Current time: Wed Aug 11 08:12:10 -12 2021
I: pbuilder-time-stamp: 1628712730