Wed Mar 12 04:21:27 UTC 2025 I: starting to build libncl/trixie/i386 on jenkins on '2025-03-12 04:21'
Wed Mar 12 04:21:27 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/58416/console.log
Wed Mar 12 04:21:27 UTC 2025 I: Downloading source for trixie/libncl=2.1.21+git20210811.b1213a7-6
--2025-03-12 04:21:27-- http://deb.debian.org/debian/pool/main/libn/libncl/libncl_2.1.21%2bgit20210811.b1213a7-6.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2422 (2.4K) [text/prs.lines.tag]
Saving to: ‘libncl_2.1.21+git20210811.b1213a7-6.dsc’
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2025-03-12 04:21:27 (277 MB/s) - ‘libncl_2.1.21+git20210811.b1213a7-6.dsc’ saved [2422/2422]
Wed Mar 12 04:21:27 UTC 2025 I: libncl_2.1.21+git20210811.b1213a7-6.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: libncl
Binary: ncl-tools, libncl2, libncl-dev
Architecture: any
Version: 2.1.21+git20210811.b1213a7-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/mtholder/ncl
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/libncl
Vcs-Git: https://salsa.debian.org/med-team/libncl.git
Testsuite: autopkgtest
Testsuite-Triggers: build-essential
Build-Depends: debhelper-compat (= 13), d-shlibs, python3
Package-List:
libncl-dev deb libdevel optional arch=any
libncl2 deb libs optional arch=any
ncl-tools deb science optional arch=any
Checksums-Sha1:
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2a3b3d70a9f3e915a800ec62f93c27861d882dc8 20292 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz
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Files:
a3af41d99fe04586c1f61bc942c5614b 544032 libncl_2.1.21+git20210811.b1213a7.orig.tar.xz
c17d9c09d67787b7821f7ae519aebab4 20292 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz
Dgit: 9623cd3f49fcc435d9b3803296d8fbc9fd7dff1c debian archive/debian/2.1.21+git20210811.b1213a7-6 https://git.dgit.debian.org/libncl
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Wed Mar 12 04:21:27 UTC 2025 I: Checking whether the package is not for us
Wed Mar 12 04:21:27 UTC 2025 I: Starting 1st build on remote node ionos6-i386.debian.net.
Wed Mar 12 04:21:27 UTC 2025 I: Preparing to do remote build '1' on ionos6-i386.debian.net.
Wed Mar 12 04:26:15 UTC 2025 I: Deleting $TMPDIR on ionos6-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Mon Apr 13 22:44:29 -12 2026
I: pbuilder-time-stamp: 1776163469
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [libncl_2.1.21+git20210811.b1213a7-6.dsc]
I: copying [./libncl_2.1.21+git20210811.b1213a7.orig.tar.xz]
I: copying [./libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./libncl_2.1.21+git20210811.b1213a7-6.dsc: unsupported subcommand
dpkg-source: info: extracting libncl in libncl-2.1.21+git20210811.b1213a7
dpkg-source: info: unpacking libncl_2.1.21+git20210811.b1213a7.orig.tar.xz
dpkg-source: info: unpacking libncl_2.1.21+git20210811.b1213a7-6.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
dpkg-source: info: applying python3.11.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/62066/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='424e7996f12244488953b6857d4fe46c'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='62066'
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/r-b-build.ncyHCGAK/pbuilderrc_iOrO --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ncyHCGAK/b1 --logfile b1/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos6-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/62066/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: i386
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 ... 19787 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} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{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, 45 newly installed, 0 to remove and 0 not upgraded.
Need to get 27.4 MB of archives. After unpacking 103 MB will be used.
Writing extended state information...
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Get: 3 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.2-1 [27.1 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 13.0.0 [29.3 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2025a-2 [259 kB]
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Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.2-1 [10.0 kB]
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Get: 15 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-7 [301 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 d-shlibs all 0.109 [11.1 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-4 [539 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 37 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Fetched 27.4 MB in 0s (91.9 MB/s)
Preconfiguring packages ...
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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Current default time zone: 'Etc/UTC'
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I: Building the package
I: Running cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ && 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+git20210811.b1213a7-6_source.changes
dpkg-buildpackage: info: source package libncl
dpkg-buildpackage: info: source version 2.1.21+git20210811.b1213a7-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
dh_clean
find . -name ".roundTripNCL*" -delete
make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'.
libtoolize: copying file 'config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'.
libtoolize: copying file 'config/libtool.m4'
libtoolize: copying file 'config/ltoptions.m4'
libtoolize: copying file 'config/ltsugar.m4'
libtoolize: copying file 'config/ltversion.m4'
libtoolize: copying file 'config/lt~obsolete.m4'
configure.ac:28: warning: The macro 'AC_PROG_LIBTOOL' is obsolete.
configure.ac:28: You should run autoupdate.
config/libtool.m4:100: AC_PROG_LIBTOOL is expanded from...
configure.ac:28: the top level
configure.ac:42: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:42: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
config/ax_cxx_flags.m4:5: AX_CXXFLAGS is expanded from...
configure.ac:42: the top level
configure.ac:124: warning: The macro 'AC_HEADER_STDC' is obsolete.
configure.ac:124: You should run autoupdate.
./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from...
configure.ac:124: the top level
configure.ac:155: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:155: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:155: the top level
configure.ac:167: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:167: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:167: the top level
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/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
dh_auto_configure -- --with-constfuncs=yes
./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-constfuncs=yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking xargs -n works... yes
checking whether UID '1111' is supported by ustar format... yes
checking whether GID '1111' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether ln -s works... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /usr/bin/sed
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checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
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checking how to recognize dependent libraries... pass_all
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
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checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
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checking whether to build static libraries... yes
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
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checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether C++ compiler works... yes
checking for egrep... (cached) /usr/bin/grep -E
checking for float.h... yes
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checking for _Bool... no
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checking for an ANSI C-conforming const... yes
checking for inline... inline
checking whether struct tm is in sys/time.h or time.h... time.h
checking for sys/time.h... yes
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checking for strtol... yes
checking for python3... /usr/bin/python3
checking python3 module: subprocess... yes
checking whether make sets $(MAKE)... (cached) yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating example/Makefile
config.status: creating example/basiccmdline/Makefile
config.status: creating example/check-taxo-nodes/Makefile
config.status: creating example/compressor/Makefile
config.status: creating example/find-unsupported-edges/Makefile
config.status: creating example/gapcode/Makefile
config.status: creating example/ot-subtree/Makefile
config.status: creating example/ot-tree-inspect/Makefile
config.status: creating example/nclsimplest/Makefile
config.status: creating example/ncltest/Makefile
config.status: creating example/normalizer/Makefile
config.status: creating example/patristic/Makefile
config.status: creating example/phylobaseinterface/Makefile
config.status: creating example/polytomy-count/Makefile
config.status: creating example/outdeg1count/Makefile
config.status: creating example/splitsinfile/Makefile
config.status: creating example/subsetter/Makefile
config.status: creating example/translate/Makefile
config.status: creating ncl/Makefile
config.status: creating test/Makefile
config.status: creating nclv2.1.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
dh_auto_build
make -j22
make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make all-recursive
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
Making all in ncl
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl'
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscharactersblock.lo nxscharactersblock.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscxxdiscretematrix.lo nxscxxdiscretematrix.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdatablock.lo nxsdatablock.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdistancesblock.lo nxsdistancesblock.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsexception.lo nxsexception.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsmultiformat.lo nxsmultiformat.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxspublicblocks.lo nxspublicblocks.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsreader.lo nxsreader.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxssetreader.lo nxssetreader.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsstring.lo nxsstring.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstoken.lo nxstoken.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsassumptionsblock.cpp -fPIC -DPIC -o .libs/nxsassumptionsblock.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -fPIC -DPIC -o .libs/nxsblock.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -fPIC -DPIC -o .libs/nxsmultiformat.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -fPIC -DPIC -o .libs/nxscxxdiscretematrix.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -fPIC -DPIC -o .libs/nxstoken.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -fPIC -DPIC -o .libs/nxsstring.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxspublicblocks.h:24,
from ../ncl/nxsmultiformat.h:25,
from nxsmultiformat.cpp:50:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from nxsmultiformat.cpp:48:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from nxsblock.cpp:21:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from ../ncl/nxsdefs.h:22,
from nxsblock.cpp:20:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxstaxablock.h:23,
from ../ncl/nxstreesblock.h:25,
from nxstreesblock.cpp:23:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from nxstreesblock.cpp:20:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxstaxablock.h:23,
from ../ncl/nxscharactersblock.h:29,
from ../ncl/nxsdatablock.h:23,
from nxsdatablock.cpp:20:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from ../ncl/nxscharactersblock.h:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxstaxablock.h:23,
from ../ncl/nxscharactersblock.h:29,
from nxscharactersblock.cpp:26:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/iomanip:42,
from nxscharactersblock.cpp:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsreader.h:24,
from nxsreader.cpp:26:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from nxsreader.cpp:21:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxspublicblocks.h:24,
from nxspublicblocks.cpp:24:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from nxspublicblocks.cpp:22:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxstaxablock.h:23,
from nxstaxablock.cpp:20:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from ../ncl/nxsdefs.h:22,
from ../ncl/nxstaxablock.h:22:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from nxsexception.cpp:20:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxstaxablock.h:23,
from ../ncl/nxsunalignedblock.h:24,
from nxsunalignedblock.cpp:21:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/functional:49,
from ../ncl/nxsstring.h:26:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from ../ncl/nxsdefs.h:22,
from ../ncl/nxsunalignedblock.h:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxstoken.h:23,
from nxstoken.cpp:22:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from nxstoken.cpp:21:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxstaxablock.h:23,
from ../ncl/nxscharactersblock.h:29,
from ../ncl/nxscxxdiscretematrix.h:28,
from nxscxxdiscretematrix.cpp:20:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/streambuf:43,
from /usr/include/c++/14/bits/streambuf_iterator.h:35,
from /usr/include/c++/14/iterator:66,
from nxscxxdiscretematrix.cpp:19:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxstaxablock.h:23,
from ../ncl/nxstaxaassociationblock.h:23,
from nxstaxaassociationblock.cpp:25:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/iomanip:42,
from nxstaxaassociationblock.cpp:20:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxsassumptionsblock.h:26,
from nxsassumptionsblock.cpp:22:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/iomanip:42,
from nxsassumptionsblock.cpp:19:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxsblock.h:24,
from ../ncl/nxstaxablock.h:23,
from ../ncl/nxsdistancesblock.h:24,
from nxsdistancesblock.cpp:23:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/iomanip:42,
from nxsdistancesblock.cpp:19:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from nxsstring.cpp:25:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from ../ncl/nxsdefs.h:22,
from nxsstring.cpp:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../ncl/nxsexception.h:23,
from ../ncl/nxstoken.h:23,
from ../ncl/nxssetreader.h:23,
from nxssetreader.cpp:20:
../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from ../ncl/nxssetreader.h:22:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -o nxstaxaassociationblock.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -o nxsunalignedblock.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -version-info 2:0:0 -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/i386-linux-gnu nxsassumptionsblock.lo nxsblock.lo nxscharactersblock.lo nxscxxdiscretematrix.lo nxsdatablock.lo nxsdistancesblock.lo nxsexception.lo nxsmultiformat.lo nxspublicblocks.lo nxsreader.lo nxssetreader.lo nxsstring.lo nxstaxablock.lo nxstaxaassociationblock.lo nxstoken.lo nxstreesblock.lo nxsunalignedblock.lo
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/14/crtbeginS.o .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxscxxdiscretematrix.o .libs/nxsdatablock.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsmultiformat.o .libs/nxspublicblocks.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstaxaassociationblock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -L/usr/lib/gcc/i686-linux-gnu/14 -L/usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/14/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/14/crtendS.o /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -fstack-protector-strong -Werror=format-security -O3 -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0
libtool: link: (cd ".libs" && rm -f "libncl.so.2" && ln -s "libncl.so.2.0.0" "libncl.so.2")
libtool: link: (cd ".libs" && rm -f "libncl.so" && ln -s "libncl.so.2.0.0" "libncl.so")
libtool: link: ar cr .libs/libncl.a nxsassumptionsblock.o nxsblock.o nxscharactersblock.o nxscxxdiscretematrix.o nxsdatablock.o nxsdistancesblock.o nxsexception.o nxsmultiformat.o nxspublicblocks.o nxsreader.o nxssetreader.o nxsstring.o nxstaxablock.o nxstaxaassociationblock.o nxstoken.o nxstreesblock.o nxsunalignedblock.o
libtool: link: ranlib .libs/libncl.a
libtool: link: ( cd ".libs" && rm -f "libncl.la" && ln -s "../libncl.la" "libncl.la" )
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl'
Making all in example
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
Making all in basiccmdline
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o basiccmdline.o basiccmdline.cpp
In file included from ../../ncl/ncl.h:79,
from basiccmdline.cpp:20:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/basiccmdline basiccmdline.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline'
Making all in check-taxo-nodes
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o checktaxonnodes-checktaxonnodes.o `test -f 'checktaxonnodes.cpp' || echo './'`checktaxonnodes.cpp
In file included from ../../ncl/ncl.h:79,
from checktaxonnodes.cpp:20:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes'
Making all in compressor
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSCharacterCompressor-compressor.o `test -f 'compressor.cpp' || echo './'`compressor.cpp
In file included from ../../ncl/nxsexception.h:23,
from ../../ncl/nxsblock.h:24,
from ../../ncl/nxstaxablock.h:23,
from ../../ncl/nxscharactersblock.h:29,
from ../../ncl/nxscxxdiscretematrix.h:28,
from compressor.cpp:4:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from compressor.cpp:1:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor'
Making all in find-unsupported-edges
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o findunsupportededges-findunsupportededges.o `test -f 'findunsupportededges.cpp' || echo './'`findunsupportededges.cpp
In file included from ../../ncl/ncl.h:79,
from findunsupportededges.cpp:20:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges'
Making all in gapcode
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -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 ../../ncl/ncl.h:79,
from gapcode.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode'
Making all in nclsimplest
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest'
g++ -DHAVE_CONFIG_H -I. -I../.. -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nclsimplest.o nclsimplest.cpp
In file included from ../../ncl/ncl.h:79,
from nclsimplest.cpp:1:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/nclsimplest nclsimplest.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest'
Making all in ncltest
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o ncltest.o ncltest.cpp
In file included from ../../ncl/ncl.h:79,
from ncltest.cpp:20:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/ncltest ncltest.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
Making all in normalizer
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o normalizer.o normalizer.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_VALIDATE_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSvalidator-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DMULTIFILE_NEXUS_READER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp
In file included from ../../ncl/ncl.h:79,
from converter.cpp:48:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from us2ml.cpp:22:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from normalizer.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from normalizer.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from us2ml.cpp:22:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from normalizer.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from normalizer.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from normalizer.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from normalizer.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so
normalizer.cpp:102:14: warning: 'substituteSafeTaxaLabels' violates the C++ One Definition Rule [-Wodr]
102 | void substituteSafeTaxaLabels(PublicNexusReader & reader, std::string filepath, bool evenTrivial);
| ^
converter.cpp:140:6: note: return value type mismatch
140 | bool substituteSafeTaxaLabels(PublicNexusReader &nexusReader, std::string filepath, bool evenTrivial)
| ^
converter.cpp:140:6: note: type 'bool' should match type 'void'
converter.cpp:140:6: note: 'substituteSafeTaxaLabels' was previously declared here
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
Making all in ot-subtree
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otsubtree-otsubtree.o `test -f 'otsubtree.cpp' || echo './'`otsubtree.cpp
In file included from ../../ncl/ncl.h:79,
from otsubtree.cpp:20:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree'
Making all in ot-tree-inspect
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -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
In file included from ../../ncl/ncl.h:79,
from ot_tree_inspect.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect'
Making all in outdeg1count
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o outdeg1count-outdeg1count.o `test -f 'outdeg1count.cpp' || echo './'`outdeg1count.cpp
In file included from ../../ncl/ncl.h:79,
from outdeg1count.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count'
Making all in patristic
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o patristic.o patristic.cpp
In file included from ../../ncl/ncl.h:79,
from patristic.cpp:33:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic'
Making all in phylobaseinterface
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLInterface.o NCLInterface.cpp
In file included from ../../ncl/ncl.h:79,
from NCLInterface.cpp:24:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface'
Making all in polytomy-count
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -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
In file included from ../../ncl/ncl.h:79,
from polytomy_count.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count'
Making all in splitsinfile
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStosplits-splitsinfile.o `test -f 'splitsinfile.cpp' || echo './'`splitsinfile.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStosplits-splitsstructs.o `test -f 'splitsstructs.cpp' || echo './'`splitsstructs.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsinfile.o splitsinfile.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp
In file included from ../../ncl/nxsexception.h:23,
from ../../ncl/nxsblock.h:24,
from ../../ncl/nxstaxablock.h:23,
from ../../ncl/nxstreesblock.h:25,
from splitsstructs.h:9,
from splitsstructs.cpp:1:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from splitsstructs.h:3:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/nxsexception.h:23,
from ../../ncl/nxsblock.h:24,
from ../../ncl/nxstaxablock.h:23,
from ../../ncl/nxstreesblock.h:25,
from splitsstructs.h:9,
from splitsstructs.cpp:1:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from splitsstructs.h:3:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from splitsinfile.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../ncl/ncl.h:79,
from splitsinfile.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile'
Making all in subsetter
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSsubsetter-subsetter.o `test -f 'subsetter.cpp' || echo './'`subsetter.cpp
In file included from ../../ncl/nxsexception.h:23,
from ../../ncl/nxsblock.h:24,
from ../../ncl/nxspublicblocks.h:24,
from ../../ncl/nxsmultiformat.h:25,
from subsetter.cpp:4:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from subsetter.cpp:1:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter'
Making all in translate
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -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 ../../ncl/ncl.h:79,
from translateNuc.cpp:46:
../../ncl/nxsstring.h:266:17: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
266 | : public std::binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../../ncl/ncl.h:45:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
Making all in test
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test'
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
dh_auto_test
make -j22 check "TESTSUITEFLAGS=-j22 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
Making check in ncl
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl'
Making check in example
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
Making check in basiccmdline
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline'
Making check in check-taxo-nodes
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes'
Making check in compressor
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor'
Making check in find-unsupported-edges
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges'
Making check in gapcode
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode'
Making check in nclsimplest
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest'
Making check in ncltest
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
make check-local
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
/usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/ncltest/ncltest ../../test/OldValidIn ../../test/OldValidOut
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest/ncltest" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/OldValidIn/m.nex"
[Reading -s2 ]
[Reading -s2 ]
storing read block: TAXA
storing read block: CHARACTERS
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest/ncltest succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/OldValidIn/m.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest/ncltest" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest/ncltest succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/OldValidOut/m.nex
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
Making check in normalizer
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
make check-local
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
/usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/characters.nex ../../test/data
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/characters.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/characters.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/characters.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/characters.nex
/usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/sample.tre ../../test/data
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/sample.tre"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/sample.tre ]
Executing
storing read block: PAUP
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/sample.tre
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/sample.tre"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/sample.tre ]
Executing
storing read block: PAUP
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/sample.tre
/usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/m.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/m.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/m.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/m.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/m.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: SETS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/m.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/cynmix.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/cynmix.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: ASSUMPTIONS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: SETS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/charsets.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/charsets.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/charsets.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/charsets.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-rake.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-rake.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-rake.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-rake.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex ]
Executing
storing read block: TAXA
storing read block: TAXA
storing read block: TAXAASSOCIATION
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex ]
Executing
storing read block: TAXA
storing read block: TAXA
storing read block: TAXAASSOCIATION
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex ]
Executing
storing read block: TAXA
storing read block: DISTANCES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/distances.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/distances.nex ]
Executing
storing read block: TAXA
storing read block: DISTANCES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/distances.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex ]
Executing
storing read block: TAXA
storing read block: UNALIGNED
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex ]
Executing
storing read block: TAXA
storing read block: UNALIGNED
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/adh.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/adh.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/adh.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/adh.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/adh.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/adh.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/parens_intree.tre"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/parens_intree.tre ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/parens_intree.tre
/usr/bin/python3 ../../test/roundTripNCLTest.py -x ../../example/normalizer/NEXUSnormalizer ../../test/funkyValidIn ../../test/funkyValidOut
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidIn/choke.tre"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidIn/choke.tre ]
Executing
Warning:
A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
at line 5, column (approximately) 6 (file position 74)
storing implied block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidIn/choke.tre
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidOut/choke.tre"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidOut/choke.tre ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidOut/choke.tre
/usr/bin/python3 ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/phyliptree_simple.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/phyliptree_simple.phy ]
Executing
storing implied block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/phyliptree_simple.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/phyliptree_simple.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/phyliptree_simple.phy ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/phyliptree_simple.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/relaxedphyliptree_q.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/relaxedphyliptree_q.phy ]
Executing
storing implied block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/relaxedphyliptree_q.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/relaxedphyliptree_q.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/relaxedphyliptree_q.phy ]
Executing
storing read block: TAXA
storing read block: TREES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/relaxedphyliptree_q.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot.aln"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot.aln ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot.aln
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot.aln"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot.aln ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot.aln
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln ]
Executing
storing implied block: TAXA
storing read block: DATA
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln ]
Executing
storing read block: TAXA
storing read block: CHARACTERS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln
/usr/bin/python3 ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/aarelaxedphylip_rana.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/aarelaxedphylip_rana.phy ]
Executing
Error:
Sequence longer than 1976 found for taxon temporariaDMH84R1. The character "o" was found, and will be ignored. If the file position of this error corresponds to sequences for the next taxon in the matrix, then that is an indication that the sequences for taxon temporariaDMH84R1 are too short.
at line 3, column (approximately) 2 (and file position 2011)
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy ]
Executing
Error:
Illegal state code "q" found when reading site 2 for taxon grylioMVZ175945
at line 12, column (approximately) 28 (and file position 20065)
/usr/bin/python3 ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer
/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/.debhelper/generated/_source/home/.ncl_round_triprc does not exist. Test stepped skipped.
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
Making check in ot-subtree
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree'
Making check in ot-tree-inspect
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect'
Making check in outdeg1count
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count'
Making check in patristic
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic'
Making check in phylobaseinterface
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface'
Making check in polytomy-count
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count'
Making check in splitsinfile
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile'
Making check in subsetter
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter'
Making check in translate
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
make check-local
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
/usr/bin/python3 ../../test/roundTripNCLTest.py -o ../../example/translate/NEXUStranslate ../../test/TranslateIn ../../test/TranslateOut
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: CODONS
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex
"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex"
[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: MRBAYES
../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
Making check in test
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test'
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
make -j1 install DESTDIR=/build/reproducible-path/libncl-2.1.21\+git20210811.b1213a7/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
Making install in ncl
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl'
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl'
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu'
/bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/libncl.so.2.0.0
libtool: install: (cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libncl.so.2.0.0 libncl.so.2 || { rm -f libncl.so.2 && ln -s libncl.so.2.0.0 libncl.so.2; }; })
libtool: install: (cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libncl.so.2.0.0 libncl.so || { rm -f libncl.so && ln -s libncl.so.2.0.0 libncl.so; }; })
libtool: install: /usr/bin/install -c .libs/libncl.lai /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/libncl.la
libtool: install: /usr/bin/install -c .libs/libncl.a /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/libncl.a
libtool: install: chmod 644 /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/libncl.a
libtool: install: ranlib /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/libncl.a
libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu'
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/include/ncl'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl'
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl'
Making install in example
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
Making install in basiccmdline
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline'
Making install in check-taxo-nodes
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes'
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/checktaxonnodes /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/checktaxonnodes
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes'
Making install in compressor
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor'
Making install in find-unsupported-edges
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges'
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/findunsupportededges /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/findunsupportededges
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges'
Making install in gapcode
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode'
Making install in nclsimplest
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest'
Making install in ncltest
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest'
Making install in normalizer
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/NEXUSnormalizer /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/NEXUSnormalizer
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/NEXUSvalidator /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/NEXUSvalidator
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/NCLconverter /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/NCLconverter
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer'
Making install in ot-subtree
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree'
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/otsubtree /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/otsubtree
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree'
Making install in ot-tree-inspect
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect'
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/otTreeInspect /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/otTreeInspect
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect'
Making install in outdeg1count
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count'
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin'
libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/outdeg1count /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/outdeg1count
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count'
Making install in patristic
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic'
Making install in phylobaseinterface
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface'
Making install in polytomy-count
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count'
Making install in splitsinfile
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile'
Making install in subsetter
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter'
Making install in translate
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate'
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example'
Making install in test
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test'
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test'
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test'
make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 nclv2.1.pc '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig'
make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
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/i386-linux-gnu/pkgconfig \
debian/tmp/usr/lib/*/libncl.so
Library package automatic movement utility
set -e
install -d -m 755 debian/libncl-dev/usr/lib/i386-linux-gnu
install -d -m 755 debian/libncl2/usr/lib/i386-linux-gnu
mv debian/tmp/usr/lib/i386-linux-gnu/libncl.a debian/libncl-dev/usr/lib/i386-linux-gnu
mv debian/tmp/usr/lib/i386-linux-gnu/libncl.la debian/libncl-dev/usr/lib/i386-linux-gnu || true
mv debian/tmp/usr/lib/i386-linux-gnu/libncl.so debian/libncl-dev/usr/lib/i386-linux-gnu
mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/i386-linux-gnu
mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/i386-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/i386-linux-gnu
PKGDEV=libncl-dev
PKGSHL=libncl2
install -d -m 755 debian/libncl-dev/usr/include/ncl
mv debian/tmp/usr/include/ncl/*.h debian/libncl-dev/usr/include/ncl
install -d -m 755 debian/libncl-dev/usr/lib/i386-linux-gnu/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libncl-dev/usr/lib/i386-linux-gnu/pkgconfig
rm -f debian/tmp/usr/include/ncl/nxsblock.cpp
make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: Depends field of package libncl-dev: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb'.
dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20210811.b1213a7-6_i386.deb'.
dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20210811.b1213a7-6_i386.deb'.
dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb'.
dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20210811.b1213a7-6_i386.deb'.
dpkg-genbuildinfo --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo
dpkg-genchanges --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
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/62066 and its subdirectories
I: Current time: Mon Apr 13 22:49:11 -12 2026
I: pbuilder-time-stamp: 1776163751
Wed Mar 12 04:26:15 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net.
Wed Mar 12 04:26:15 UTC 2025 I: Preparing to do remote build '2' on ionos12-i386.debian.net.
Wed Mar 12 04:34:37 UTC 2025 I: Deleting $TMPDIR on ionos12-i386.debian.net.
Wed Mar 12 04:34:37 UTC 2025 I: libncl_2.1.21+git20210811.b1213a7-6_i386.changes:
Format: 1.8
Date: Sun, 25 Aug 2024 11:33:47 +0200
Source: libncl
Binary: libncl-dev libncl2 libncl2-dbgsym ncl-tools ncl-tools-dbgsym
Architecture: i386
Version: 2.1.21+git20210811.b1213a7-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
libncl-dev - NEXUS Class Library (static lib and header files)
libncl2 - NEXUS Class Library
ncl-tools - tools to deal with NEXUS files
Closes: 1015505 1075191
Changes:
libncl (2.1.21+git20210811.b1213a7-6) unstable; urgency=medium
.
* d/rules: forcefully run LTO builds.
* d/libncl2.symbols.amd64: mark symbols leaked by the compiler optional.
(Closes: #1015505, #1075191)
* d/control: add myself to uploaders.
* d/control: declare compliance to standards version 4.7.0.
Checksums-Sha1:
61539d3a046c165b4a7630b380a2bf0dd5ea3437 642212 libncl-dev_2.1.21+git20210811.b1213a7-6_i386.deb
5efb1a559b502be50a52ef69ca200c9e116304ef 6094472 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
7cd711607c77fab60f2f632216c03007a82e0cf6 406196 libncl2_2.1.21+git20210811.b1213a7-6_i386.deb
b8e96a13a357a073218e3283542aab87e5cf4d46 6809 libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo
3dd28797d39a43b6c0fb83f1e78e8a1641c351a6 4589032 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
ddc0cb07f7c3fd64d601b81af500ef8535e36618 198488 ncl-tools_2.1.21+git20210811.b1213a7-6_i386.deb
Checksums-Sha256:
0ee5c82d123d9f37918e9fb04e44ea1fb73898265592faae9d21171eeafd82eb 642212 libncl-dev_2.1.21+git20210811.b1213a7-6_i386.deb
19fd0b751f386e9dbd132f8255ff49c13c12fcf659fd9ac5c817dd842d15cfdb 6094472 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
cab2b701b9a275f7ec252bd7b40aa4329d5b4479467a539d09e85f4474d0f2ae 406196 libncl2_2.1.21+git20210811.b1213a7-6_i386.deb
b7dfa73b42a36de3f7e993102dbc7c20ac1fb2e2020b56ff09d20683d81b596b 6809 libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo
b55f3006daf5ec584630857ad04224753f6ea0606078eb1b9d23e6641326ea47 4589032 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
eb225e8d144c9e7c41cd0b159f66c1fef2a5deae771f95611f9a97a7b937f507 198488 ncl-tools_2.1.21+git20210811.b1213a7-6_i386.deb
Files:
493b924641068c0be7fb6ac04414f8ed 642212 libdevel optional libncl-dev_2.1.21+git20210811.b1213a7-6_i386.deb
284a912f0264c31c95c44ac8d929d2ef 6094472 debug optional libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
f88d015c12322127fe4a5c3facc26988 406196 libs optional libncl2_2.1.21+git20210811.b1213a7-6_i386.deb
3d7e0de9955cf4ca0816cccc1a3b1a4d 6809 science optional libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo
9a360384fff76b2acc241271ce5742f4 4589032 debug optional ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
53fca30912cdc0cf3799aeb85c41123a 198488 science optional ncl-tools_2.1.21+git20210811.b1213a7-6_i386.deb
Wed Mar 12 04:34:38 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_6-58416.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ncyHCGAK/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ncyHCGAK/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ncyHCGAK/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ncyHCGAK/b1/libncl_2.1.21+git20210811.b1213a7-6_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.ncyHCGAK/b2/libncl_2.1.21+git20210811.b1213a7-6_i386.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 229ms
CPU time consumed: 230ms
Wed Mar 12 04:34:39 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Wed Mar 12 04:34:39 UTC 2025 I: libncl from trixie built successfully and reproducibly on i386.
Wed Mar 12 04:34:40 UTC 2025 I: Submitting .buildinfo files to external archives:
Wed Mar 12 04:34:40 UTC 2025 I: Submitting 8.0K b1/libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo.asc
Wed Mar 12 04:34:41 UTC 2025 I: Submitting 8.0K b2/libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo.asc
Wed Mar 12 04:34:41 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Wed Mar 12 04:34:41 UTC 2025 I: Done submitting .buildinfo files.
Wed Mar 12 04:34:41 UTC 2025 I: Removing signed libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo.asc files:
removed './b1/libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo.asc'
removed './b2/libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo.asc'