Fri Dec 20 21:51:46 UTC 2024 I: starting to build libncl/unstable/i386 on jenkins on '2024-12-20 21:51'
Fri Dec 20 21:51:46 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_11/39860/console.log
Fri Dec 20 21:51:46 UTC 2024 I: Downloading source for unstable/libncl=2.1.21+git20210811.b1213a7-6
--2024-12-20 21:51:46-- 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’
0K .. 100% 396M=0s
2024-12-20 21:51:46 (396 MB/s) - ‘libncl_2.1.21+git20210811.b1213a7-6.dsc’ saved [2422/2422]
Fri Dec 20 21:51:46 UTC 2024 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
Checksums-Sha256:
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7be3f38ea803136f6776b180235681864d28775710e19b2cec89860bdaea0595 20292 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz
Files:
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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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Fri Dec 20 21:51:46 UTC 2024 I: Checking whether the package is not for us
Fri Dec 20 21:51:46 UTC 2024 I: Starting 1st build on remote node infom08-i386.debian.net.
Fri Dec 20 21:51:46 UTC 2024 I: Preparing to do remote build '1' on infom08-i386.debian.net.
Fri Dec 20 21:55:34 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu Jan 22 16:14:48 -12 2026
I: pbuilder-time-stamp: 1769141688
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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
gpgv: Signature made Sun Aug 25 10:18:49 2024
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libncl_2.1.21+git20210811.b1213a7-6.dsc: no acceptable signature found
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/11663/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=6 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='823733e687a3450e9b6663b33b8b952a'
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='11663'
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.2uKNnq4M/pbuilderrc_dzNY --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2uKNnq4M/b1 --logfile b1/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc'
SUDO_GID='111'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
I: uname -a
Linux infom08-i386 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/11663/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 ... 19953 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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 52 newly installed, 0 to remove and 0 not upgraded.
Need to get 27.3 MB of archives. After unpacking 104 MB will be used.
Writing extended state information...
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Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.7-1 [26.8 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024b-4 [256 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 12 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.8-3 [1968 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.8-3 [677 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.7-1 [9712 B]
Get: 22 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.7-1 [27.8 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-3 [201 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-3 [723 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 d-shlibs all 0.108 [11.0 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.22 [90.5 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 45 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 48 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-3 [1631 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 debhelper all 13.22 [919 kB]
Fetched 27.3 MB in 1s (43.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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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 build environment is sane... yes
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checking how to create a ustar tar archive... gnutar
checking whether ln -s works... yes
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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
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checking for suffix of object files... o
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checking dependency style of gcc... none
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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
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checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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checking whether the compiler supports GNU C++... yes
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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 inline... inline
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checking python3 module: subprocess... yes
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checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating example/Makefile
config.status: creating example/basiccmdline/Makefile
config.status: creating example/check-taxo-nodes/Makefile
config.status: creating example/compressor/Makefile
config.status: creating example/find-unsupported-edges/Makefile
config.status: creating example/gapcode/Makefile
config.status: creating example/ot-subtree/Makefile
config.status: creating example/ot-tree-inspect/Makefile
config.status: creating example/nclsimplest/Makefile
config.status: creating example/ncltest/Makefile
config.status: creating example/normalizer/Makefile
config.status: creating example/patristic/Makefile
config.status: creating example/phylobaseinterface/Makefile
config.status: creating example/polytomy-count/Makefile
config.status: creating example/outdeg1count/Makefile
config.status: creating example/splitsinfile/Makefile
config.status: creating example/subsetter/Makefile
config.status: creating example/translate/Makefile
config.status: creating ncl/Makefile
config.status: creating test/Makefile
config.status: creating nclv2.1.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7'
dh_auto_build
make -j6
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
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 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 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 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 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 nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o
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/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/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/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/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
| ^~~~~~~~~~~~~~~
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 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 nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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
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
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 /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
| ^~~~~~~~~~~~~~~
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 nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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
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 nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.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 ../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
| ^~~~~~~~~~~~~~~
/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
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
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
| ^~~~~~~~~~~~~~~
/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
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
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 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 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 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 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 nxsreader.cpp -o nxsreader.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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
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
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
| ^~~~~~~~~~~~~~~
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 nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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
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
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
| ^~~~~~~~~~~~~~~
/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
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
/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
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
| ^~~~~~~~~~~~~~~
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
/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
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
| ^~~~~~~~~~~~~~~
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
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
| ^~~~~~~~~~~~~~~
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
/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 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 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
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/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
| ^~~~~~~~~~~~~~~
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 nxsunalignedblock.cpp -o nxsunalignedblock.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 -flto=auto -fstack-protector-strong -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
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 ../../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 /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
| ^~~~~~~~~~~~~~~
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 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 NEXUSnormalizer normalizer.o ../../ncl/libncl.la
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
| ^~~~~~~~~~~~~~~
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
/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
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
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
/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
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
/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/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
/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
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
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 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/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.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 majrule splitsinfile.o 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
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 -j6 check "TESTSUITEFLAGS=-j6 --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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-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/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" "-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" "-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" "-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" "-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" "-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" "-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_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
"/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
/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" "-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)
"/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)
/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' in '../ncl-tools_2.1.21+git20210811.b1213a7-6_i386.deb'.
dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-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-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb'.
dpkg-deb: building package 'libncl2' in '../libncl2_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/11663 and its subdirectories
I: Current time: Thu Jan 22 16:18:32 -12 2026
I: pbuilder-time-stamp: 1769141912
Fri Dec 20 21:55:34 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net.
Fri Dec 20 21:55:34 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net.
Fri Dec 20 22:02:57 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net.
Fri Dec 20 22:02:57 UTC 2024 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:
6e19ec601d442258483f2d23fcf302d0b7d9ea31 642716 libncl-dev_2.1.21+git20210811.b1213a7-6_i386.deb
2544578e134b4f5086da208baa7366cf9b3b7fb5 6094704 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
a54a29593d20cdbeaf39924e57b5d9da8e3372c1 406748 libncl2_2.1.21+git20210811.b1213a7-6_i386.deb
c7d495833e5a251cb5e6e12d32b58645ca629837 7423 libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo
dbbbc6a6a32d16da956cdec0893d400a0e9d5b34 4589860 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
50eada11ebe24edfe940a7590f1cf5f357accea3 198296 ncl-tools_2.1.21+git20210811.b1213a7-6_i386.deb
Checksums-Sha256:
0e501d156cab2941dfc529d1c77b48f92216cb17133fd0ba9ea8f5640d196847 642716 libncl-dev_2.1.21+git20210811.b1213a7-6_i386.deb
01f2b76de276658a4d0b40c3a72f73dd6dc7697293b034460bf7b65cad1c7010 6094704 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
29750662802e10bccba6f2d9ce3ebea96fad2a4d6040b1c3285c54cdfe392855 406748 libncl2_2.1.21+git20210811.b1213a7-6_i386.deb
ddc261fb411b43c277b24577390f9768312c50484010164f7279b6a8cc733c49 7423 libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo
d2d03c14d3f80d076af419b6475dde2bf4a54561f331e26261c48c79c34ddf37 4589860 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
dc82e4cb5654fed294095483b7571573c079979c161acf3709fe0f6a87fa23ac 198296 ncl-tools_2.1.21+git20210811.b1213a7-6_i386.deb
Files:
81081c02c1de8c5b5790371fbf611390 642716 libdevel optional libncl-dev_2.1.21+git20210811.b1213a7-6_i386.deb
410de9538def09060b4cd2ba775f2058 6094704 debug optional libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
3ec08bf55063f88e6fbf64b953862104 406748 libs optional libncl2_2.1.21+git20210811.b1213a7-6_i386.deb
e40ff8785eeadc3e949b8ae963622628 7423 science optional libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo
4d5b7ef31c9c90fb41dc73e4cde810ef 4589860 debug optional ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_i386.deb
dcbd70cec163853868049572dfc1d1ff 198296 science optional ncl-tools_2.1.21+git20210811.b1213a7-6_i386.deb
Fri Dec 20 22:02:58 UTC 2024 I: diffoscope 284 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_11-39860.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2uKNnq4M/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2uKNnq4M/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2uKNnq4M/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2uKNnq4M/b1/libncl_2.1.21+git20210811.b1213a7-6_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.2uKNnq4M/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 abc.DotChangesFile
## main (total time: 0.485s)
0.485s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.143s)
0.143s 12 calls diffoscope.comparators.binary.FilesystemFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 793ms
CPU time consumed: 792ms
Fri Dec 20 22:02:59 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists.
Fri Dec 20 22:02:59 UTC 2024 I: libncl from unstable built successfully and reproducibly on i386.
Fri Dec 20 22:03:01 UTC 2024 I: Submitting .buildinfo files to external archives:
Fri Dec 20 22:03:01 UTC 2024 I: Submitting 12K b1/libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo.asc
Fri Dec 20 22:03:02 UTC 2024 I: Submitting 12K b2/libncl_2.1.21+git20210811.b1213a7-6_i386.buildinfo.asc
Fri Dec 20 22:03:02 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Fri Dec 20 22:03:02 UTC 2024 I: Done submitting .buildinfo files.
Fri Dec 20 22:03:02 UTC 2024 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'