Diff of the two buildlogs: -- --- b1/build.log 2024-12-20 21:55:34.056793636 +0000 +++ b2/build.log 2024-12-20 22:02:56.472774335 +0000 @@ -1,6 +1,6 @@ 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: Current time: Sat Dec 21 11:55:36 +14 2024 +I: pbuilder-time-stamp: 1734731736 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,53 +33,86 @@ 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: user script /srv/workspace/pbuilder/38545/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 20 21:55 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/38545/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/38545/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + 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='> ' + INVOCATION_ID=3c68fe330a6b4388ad5e6220edf51312 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=38545 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2uKNnq4M/pbuilderrc_C1Ku --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2uKNnq4M/b2 --logfile b2/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 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 + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) 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 + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/38545/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -171,7 +204,7 @@ 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) +Fetched 27.3 MB in 0s (69.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19953 files and directories currently installed.) @@ -361,8 +394,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jan 23 04:15:07 UTC 2026. -Universal Time is now: Fri Jan 23 04:15:07 UTC 2026. +Local time is now: Fri Dec 20 21:56:08 UTC 2024. +Universal Time is now: Fri Dec 20 21:56:08 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -408,7 +441,11 @@ Building tag database... -> Finished parsing the build-deps 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 +I: user script /srv/workspace/pbuilder/38545/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/38545/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -469,8 +506,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... i686-pc-linux-gnu @@ -605,73 +642,78 @@ config.status: executing libtool commands make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' dh_auto_build - make -j6 + make -j10 make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make all-recursive make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' Making all in ncl make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsassumptionsblock.lo nxsassumptionsblock.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsblock.lo nxsblock.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscharactersblock.lo nxscharactersblock.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscxxdiscretematrix.lo nxscxxdiscretematrix.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdatablock.lo nxsdatablock.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdistancesblock.lo nxsdistancesblock.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdistancesblock.lo nxsdistancesblock.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsexception.lo nxsexception.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxspublicblocks.lo nxspublicblocks.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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 nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c 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 nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c 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 nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c 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 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 nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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: + from nxsblock.cpp:21: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::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/iomanip:42, - from nxscharactersblock.cpp:23: + 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 nxsblock.cpp:21: + from ../ncl/nxstaxablock.h:23, + from ../ncl/nxsdistancesblock.h:24, + from nxsdistancesblock.cpp:23: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from ../ncl/nxsdefs.h:22, - from nxsblock.cpp:20: + from /usr/include/c++/14/iomanip:42, + from nxsdistancesblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../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: + from ../ncl/nxspublicblocks.h:24, + from nxspublicblocks.cpp:24: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::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/streambuf:43, - from /usr/include/c++/14/bits/streambuf_iterator.h:35, - from /usr/include/c++/14/iterator:66, - from nxscxxdiscretematrix.cpp:19: + 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 | ^~~~~~~~~~~~~~~ @@ -695,79 +737,70 @@ 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: + from nxsexception.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::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/iomanip:42, - from nxsassumptionsblock.cpp:19: +In file included from /usr/include/c++/14/functional:49, + from ../ncl/nxsstring.h:26: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, - from ../ncl/nxsdistancesblock.h:24, - from nxsdistancesblock.cpp:23: + from ../ncl/nxscharactersblock.h:29, + from ../ncl/nxscxxdiscretematrix.h:28, + from nxscxxdiscretematrix.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::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/iomanip:42, - from nxsdistancesblock.cpp:19: + 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 | ^~~~~~~~~~~~~~~ -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: + from ../ncl/nxsblock.h:24, + from ../ncl/nxsassumptionsblock.h:26, + from nxsassumptionsblock.cpp:22: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/functional:49, - from ../ncl/nxsstring.h:26: +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 | ^~~~~~~~~~~~~~~ -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: + from ../ncl/nxstaxablock.h:23, + from ../ncl/nxscharactersblock.h:29, + from nxscharactersblock.cpp:26: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::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 nxsmultiformat.cpp:48: + 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 ../ncl/nxspublicblocks.h:24, - from nxspublicblocks.cpp:24: + from ../ncl/nxsmultiformat.h:25, + from nxsmultiformat.cpp:50: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ @@ -776,12 +809,11 @@ 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: + 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 | ^~~~~~~~~~~~~~~ -/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -793,8 +825,10 @@ /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 nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +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 In file included from ../ncl/nxsexception.h:23, from ../ncl/nxstoken.h:23, from ../ncl/nxssetreader.h:23, @@ -812,12 +846,10 @@ /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 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 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 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nxsstring.cpp -fPIC -DPIC -o .libs/nxsstring.o In file included from nxsstring.cpp:25: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -834,9 +866,11 @@ /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 nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c 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 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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, @@ -856,9 +890,7 @@ /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 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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, @@ -876,7 +908,9 @@ 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 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 In file included from ../ncl/nxsexception.h:23, from ../ncl/nxstoken.h:23, from nxstoken.cpp:22: @@ -893,6 +927,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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, @@ -913,10 +948,11 @@ 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 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 nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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, @@ -938,7 +974,8 @@ | ^~~~~~~~~~~~~~~ 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: 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/sh ../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") @@ -966,7 +1003,7 @@ /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 +/bin/sh ../../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 @@ -987,7 +1024,7 @@ /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 +/bin/sh ../../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 @@ -1007,7 +1044,7 @@ /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 +/bin/sh ../../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 @@ -1028,7 +1065,7 @@ /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 +/bin/sh ../../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 @@ -1049,7 +1086,7 @@ /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 +/bin/sh ../../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 @@ -1070,7 +1107,7 @@ /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 +/bin/sh ../../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 @@ -1091,7 +1128,7 @@ /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 +/bin/sh ../../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 @@ -1102,16 +1139,14 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DMULTIFILE_NEXUS_READER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../ncl/ncl.h:79, - from converter.cpp:48: -../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 266 | : public std::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, @@ -1122,6 +1157,11 @@ /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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::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, @@ -1182,6 +1222,11 @@ ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ +In file included from ../../ncl/ncl.h:79, + from normalizer.cpp:46: +../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::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, @@ -1192,14 +1237,6 @@ /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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 266 | : public std::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, @@ -1210,7 +1247,11 @@ /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 converter.cpp:48: +../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::binary_function + | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from us2ml.cpp:22: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1226,11 +1267,6 @@ /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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 266 | : public std::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, @@ -1241,15 +1277,17 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/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 +/bin/sh ../../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/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 +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so +/bin/sh ../../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 +/bin/sh ../../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 +/bin/sh ../../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 normalizer.cpp:102:14: warning: 'substituteSafeTaxaLabels' violates the C++ One Definition Rule [-Wodr] 102 | void substituteSafeTaxaLabels(PublicNexusReader & reader, std::string filepath, bool evenTrivial); | ^ @@ -1258,7 +1296,6 @@ | ^ 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 @@ -1279,7 +1316,7 @@ /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 +/bin/sh ../../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 @@ -1300,7 +1337,7 @@ /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 +/bin/sh ../../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 @@ -1321,7 +1358,7 @@ /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 +/bin/sh ../../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 @@ -1342,7 +1379,7 @@ /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 +/bin/sh ../../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 @@ -1363,7 +1400,7 @@ /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 +/bin/sh ../../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 @@ -1384,7 +1421,7 @@ /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 +/bin/sh ../../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 @@ -1453,9 +1490,9 @@ /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 +/bin/sh ../../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 +/bin/sh ../../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/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 @@ -1474,7 +1511,7 @@ /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 +/bin/sh ../../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 @@ -1495,7 +1532,7 @@ /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 +/bin/sh ../../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' @@ -1511,7 +1548,7 @@ 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 -j10 check "TESTSUITEFLAGS=-j10 --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' @@ -1605,36 +1642,94 @@ 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 ] +"/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/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/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) 10 (file position 26) +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/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 ] +../../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/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 ] +../../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/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/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-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 ] +../../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-dos.nex +../../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/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/kim.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex ] Executing @@ -1649,32 +1744,50 @@ 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 ] +"/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: 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 ] +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/protein.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.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 ] +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 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 ] +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 -../../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 ] +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/charsets.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/charsets.nex ] Executing Warning: @@ -1682,14 +1795,11 @@ 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 ] +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: @@ -1697,60 +1807,37 @@ 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 ] +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/charsets.nex +"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] Executing - -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: 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/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 ] +../../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/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 ] +../../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 -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 ] +../../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 -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 +../../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/associates.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex ] Executing @@ -1765,80 +1852,64 @@ 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 ] +"/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: 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 ] +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 -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 ] +../../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/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: 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 ] +../../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/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 ] +../../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/characters.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.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 ] + +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: 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 +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/linktest.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex ] Executing @@ -1901,48 +1972,42 @@ 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 ] +"/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 -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 ] +../../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 -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 ] +../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex +"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES -../../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 ] +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 -../../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 +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/partitions.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex ] Executing @@ -1969,162 +2034,134 @@ 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 ] +"/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/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 ] +../../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/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 ] +../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex +"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex ] Executing storing read block: TAXA -storing read block: 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 ] +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: 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 ] +storing read block: DISTANCES +../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/distances.nex +"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex ] Executing storing read block: TAXA -storing read block: 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 ] +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: 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 ] +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/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 -../../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 +storing read block: CODONS 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 + An * is ignored in a CHARSET command +at line 67, column (approximately) 46 (file position 929) Warning: - Skipping command: blockid -at line 6, column (approximately) 13 (file position 188) + 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 -../../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 ] +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/anolis.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.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 ] +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: 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 ] +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/bglobin.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.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 ] +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: 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 ] +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/treeswithouttaxa.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex ] Executing -storing read block: TAXA -storing read block: CHARACTERS + +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/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 ] +../../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: 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 ] +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/primates.nex" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.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 ] +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 - -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 ] +../../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/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 @@ -2133,18 +2170,18 @@ Warning: An * is ignored in a CHARSET command -at line 67, column (approximately) 46 (file position 929) +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 968) +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/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 ] +../../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 @@ -2154,7 +2191,7 @@ 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 +../../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/parens_intree.tre" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre ] Executing @@ -2185,18 +2222,42 @@ 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 ] +"/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/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 ] +../../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/dnarelaxedphylip_rana.phy +../../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" "-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" "-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 @@ -2209,30 +2270,30 @@ 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 ] +"/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_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 ] +../../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_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 ] +../../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" "-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/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 ] +../../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/aarelaxedphylip_rana.phy +../../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" "-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 @@ -2245,30 +2306,6 @@ 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 @@ -2306,18 +2343,18 @@ 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) +"/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy" +[Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy ] +Executing +Error: + Illegal state code "q" found when reading site 2 for taxon grylioMVZ175945 +at line 12, column (approximately) 28 (and file position 20065) /usr/bin/python3 ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/.debhelper/generated/_source/home/.ncl_round_triprc does not exist. Test stepped skipped. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' @@ -2395,7 +2432,7 @@ 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' + /bin/sh ../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; }; }) @@ -2421,7 +2458,7 @@ 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' + /bin/sh ../../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'. @@ -2438,7 +2475,7 @@ 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' + /bin/sh ../../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'. @@ -2469,7 +2506,7 @@ 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' + /bin/sh ../../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' @@ -2483,7 +2520,7 @@ 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' + /bin/sh ../../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'. @@ -2493,7 +2530,7 @@ 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' + /bin/sh ../../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'. @@ -2503,7 +2540,7 @@ 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' + /bin/sh ../../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'. @@ -2617,11 +2654,11 @@ 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 'libncl2' in '../libncl2_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-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-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) @@ -2629,12 +2666,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/38545/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/38545/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/11663 and its subdirectories -I: Current time: Thu Jan 22 16:18:32 -12 2026 -I: pbuilder-time-stamp: 1769141912 +I: removing directory /srv/workspace/pbuilder/38545 and its subdirectories +I: Current time: Sat Dec 21 12:02:55 +14 2024 +I: pbuilder-time-stamp: 1734732175