Diff of the two buildlogs: -- --- b1/build.log 2020-03-14 11:11:06.133066042 +0000 +++ b2/build.log 2020-03-14 11:13:55.113588088 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Mar 13 22:58:16 -12 2020 -I: pbuilder-time-stamp: 1584183496 +I: Current time: Sat Apr 17 07:34:07 +14 2021 +I: pbuilder-time-stamp: 1618594447 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Mar 7 06:17:52 2019 -12 +gpgv: Signature made Fri Mar 8 08:17:52 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,6 +32,18 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/58725/tmp/hooks/D01_modify_environment starting +disorder-fs debug: Running on profitbricks-build16-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/58725/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -120,7 +132,7 @@ Get: 47 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] -Fetched 25.5 MB in 17s (1516 kB/s) +Fetched 25.5 MB in 0s (84.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19231 files and directories currently installed.) @@ -341,7 +353,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libncl-2.1.21+git20180827.c71b264/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/libncl-2.1.21+git20180827.c71b264/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20180827.c71b264-2 dpkg-buildpackage: info: source distribution unstable @@ -382,8 +394,8 @@ 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 @@ -523,64 +535,64 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' dh_auto_build - make -j10 + make -j18 make[1]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' make all-recursive make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' Making all in ncl make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' -/bin/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/libncl-2.1.21+git20180827.c71b264=. -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.. 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../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -version-info 2:0:0 -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/i386-linux-gnu nxsassumptionsblock.lo nxsblock.lo nxscharactersblock.lo nxscxxdiscretematrix.lo nxsdatablock.lo nxsdistancesblock.lo nxsexception.lo nxsmultiformat.lo nxspublicblocks.lo nxsreader.lo nxssetreader.lo nxsstring.lo nxstaxablock.lo nxstaxaassociationblock.lo nxstoken.lo nxstreesblock.lo nxsunalignedblock.lo +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -version-info 2:0:0 -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/i386-linux-gnu nxsassumptionsblock.lo nxsblock.lo nxscharactersblock.lo nxscxxdiscretematrix.lo nxsdatablock.lo nxsdistancesblock.lo nxsexception.lo nxsmultiformat.lo nxspublicblocks.lo nxsreader.lo nxssetreader.lo nxsstring.lo nxstaxablock.lo nxstaxaassociationblock.lo nxstoken.lo nxstreesblock.lo nxsunalignedblock.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/8/crtbeginS.o .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxscxxdiscretematrix.o .libs/nxsdatablock.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsmultiformat.o .libs/nxspublicblocks.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstaxaassociationblock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -L/usr/lib/gcc/i686-linux-gnu/8 -L/usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/8/crtendS.o /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -O3 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libncl.so.2" && ln -s "libncl.so.2.0.0" "libncl.so.2") libtool: link: (cd ".libs" && rm -f "libncl.so" && ln -s "libncl.so.2.0.0" "libncl.so") @@ -594,43 +606,43 @@ Making all in basiccmdline make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o basiccmdline.o basiccmdline.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/basiccmdline basiccmdline.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/basiccmdline' Making all in check-taxo-nodes make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o checktaxonnodes-checktaxonnodes.o `test -f 'checktaxonnodes.cpp' || echo './'`checktaxonnodes.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' Making all in compressor make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSCharacterCompressor-compressor.o `test -f 'compressor.cpp' || echo './'`compressor.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/compressor' Making all in find-unsupported-edges make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o findunsupportededges-findunsupportededges.o `test -f 'findunsupportededges.cpp' || echo './'`findunsupportededges.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' Making all in gapcode make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSgapcode-gapcode.o `test -f 'gapcode.cpp' || echo './'`gapcode.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/gapcode' Making all in nclsimplest make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' g++ -DHAVE_CONFIG_H -I. -I../.. -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nclsimplest.o nclsimplest.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/nclsimplest nclsimplest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/nclsimplest' Making all in ncltest make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o ncltest.o ncltest.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/ncltest ncltest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ncltest' Making all in normalizer @@ -644,53 +656,53 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DMULTIFILE_NEXUS_READER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la -libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 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NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so -libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la -libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' Making all in ot-subtree make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otsubtree-otsubtree.o `test -f 'otsubtree.cpp' || echo './'`otsubtree.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' Making all in ot-tree-inspect make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otTreeInspect-ot_tree_inspect.o `test -f 'ot_tree_inspect.cpp' || echo './'`ot_tree_inspect.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' Making all in outdeg1count make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o outdeg1count-outdeg1count.o `test -f 'outdeg1count.cpp' || echo './'`outdeg1count.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' Making all in patristic make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/patristic' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o patristic.o patristic.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/patristic' Making all in phylobaseinterface make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/phylobaseinterface' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLInterface.o NCLInterface.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/phylobaseinterface' Making all in polytomy-count make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/polytomy-count' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o polytomycount-polytomy_count.o `test -f 'polytomy_count.cpp' || echo './'`polytomy_count.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/polytomy-count' Making all in splitsinfile @@ -699,21 +711,21 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStosplits-splitsstructs.o `test -f 'splitsstructs.cpp' || echo './'`splitsstructs.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsinfile.o splitsinfile.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la -libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/splitsinfile' Making all in subsetter make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/subsetter' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSsubsetter-subsetter.o `test -f 'subsetter.cpp' || echo './'`subsetter.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/subsetter' Making all in translate make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/translate' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStranslate-translateNuc.o `test -f 'translateNuc.cpp' || echo './'`translateNuc.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20180827.c71b264=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/translate' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example' @@ -729,7 +741,7 @@ make[2]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' make[1]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264' dh_auto_test - make -j10 check VERBOSE=1 + make -j18 check VERBOSE=1 make[1]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264' Making check in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' @@ -823,122 +835,104 @@ storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/data/sample.tre /usr/bin/python ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/mdata.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/mdata.nex ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex ] +Executing +storing read block: TAXA +storing read block: UNALIGNED +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex ] +Executing +storing read block: TAXA +storing read block: UNALIGNED +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/cynmix.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/cynmix.nex ] Executing storing implied block: TAXA storing read block: DATA -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/mdata.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/mdata.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/mdata.nex ] +storing read block: MRBAYES +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/cynmix.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/cynmix.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/cynmix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: SETS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/mdata.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/t.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/t.nex ] +storing read block: MRBAYES +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/cynmix.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mixed-line-endings.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/t.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/t.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/t.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mixed-line-endings.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mixed-line-endings.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/t.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/characters.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/characters.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mixed-line-endings.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/treeswithouttaxa.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/treeswithouttaxa.nex ] Executing Warning: - Skipping command: blockid -at line 13, column (approximately) 11 (file position 176) -storing read block: TAXA -storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/characters.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/characters.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/characters.nex ] + A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. +at line 3, column (approximately) 10 (file position 26) +storing implied block: TAXA +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/treeswithouttaxa.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex ] Executing - -Warning: - Skipping command: blockid -at line 6, column (approximately) 13 (file position 183) storing read block: TAXA -storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/characters.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-rake.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-rake.nex ] +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: TREES -storing read block: CODONS - -Warning: - An * is ignored in a CHARSET command -at line 67, column (approximately) 46 (file position 929) - -Warning: - An * is ignored in a CHARSET command -at line 68, column (approximately) 42 (file position 968) -storing read block: ASSUMPTIONS -storing read block: ASSUMPTIONS -storing read block: MESQUITECHARMODELS -storing read block: MESQUITE -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-rake.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-rake.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-rake.nex ] +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex ] Executing storing read block: TAXA -storing read block: CHARACTERS -storing read block: TREES -storing read block: CODONS -storing read block: SETS -storing read block: ASSUMPTIONS -storing read block: MESQUITECHARMODELS -storing read block: MESQUITE -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-rake.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/m.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/m.nex ] +storing read block: TAXA +storing read block: TAXAASSOCIATION +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex ] Executing storing read block: TAXA -storing read block: CHARACTERS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/m.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/m.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/m.nex ] +storing read block: TAXA +storing read block: TAXAASSOCIATION +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: SETS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/m.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mac.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mac.nex ] Executing @@ -953,34 +947,32 @@ storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mac.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex ] Executing storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/protein.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex ] +storing read block: DISTANCES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex ] Executing storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/protein.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/treeswithouttaxa.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/treeswithouttaxa.nex ] +storing read block: DISTANCES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/t.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/t.nex ] Executing - -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: TAXA +storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/treeswithouttaxa.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/t.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/t.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/t.nex ] Executing storing read block: TAXA +storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/treeswithouttaxa.nex +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/t.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-unix.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-unix.nex ] Executing @@ -995,36 +987,136 @@ storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-unix.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mixed-line-endings.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/dzmissing_bug.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/dzmissing_bug.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: ASSUMPTIONS +storing read block: MACCLADE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/dzmissing_bug.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/dzmissing_bug.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/dzmissing_bug.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-mixed-line-endings.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mixed-line-endings.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mixed-line-endings.nex ] +storing read block: ASSUMPTIONS +storing read block: MACCLADE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/dzmissing_bug.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/m.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/m.nex ] Executing storing read block: TAXA storing read block: CHARACTERS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/m.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/m.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/m.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: SETS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/m.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock-quotes.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock-quotes.nex ] +Executing + +Warning: + A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. +at line 3, column (approximately) 7 (file position 26) +storing implied block: TAXA storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-mixed-line-endings.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/cynmix.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/cynmix.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock-quotes.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex ] +Executing +storing read block: TAXA +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/replicase.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/replicase.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/cynmix.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/cynmix.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/cynmix.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/replicase.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/replicase.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/replicase.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/cynmix.nex +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/replicase.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock.nex ] +Executing + +Warning: + A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. +at line 3, column (approximately) 13 (file position 32) +storing implied block: TAXA +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex ] +Executing +storing read block: TAXA +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/characters.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/characters.nex ] +Executing + +Warning: + Skipping command: blockid +at line 13, column (approximately) 11 (file position 176) +storing read block: TAXA +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/characters.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/characters.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/characters.nex ] +Executing + +Warning: + Skipping command: blockid +at line 6, column (approximately) 13 (file position 183) +storing read block: TAXA +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/characters.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/charsets.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/charsets.nex ] +Executing + +Warning: + Skipping command: blockid +at line 13, column (approximately) 11 (file position 176) +storing read block: TAXA +storing read block: CHARACTERS +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/charsets.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/charsets.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/charsets.nex ] +Executing + +Warning: + Skipping command: blockid +at line 6, column (approximately) 13 (file position 183) +storing read block: TAXA +storing read block: CHARACTERS +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/charsets.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/partitions.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/partitions.nex ] Executing @@ -1051,22 +1143,34 @@ storing read block: SETS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/partitions.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock-quotes.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock-quotes.nex ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/bglobin.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/bglobin.nex ] Executing - -Warning: - A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. -at line 3, column (approximately) 7 (file position 26) storing implied block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock-quotes.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex ] +storing read block: DATA +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/bglobin.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/bglobin.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/bglobin.nex ] Executing storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock-quotes.nex +storing read block: CHARACTERS +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/bglobin.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/adh.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/adh.nex ] Executing @@ -1081,20 +1185,100 @@ storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/adh.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/paup_characters.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/paup_characters.nex ] +Executing + +Warning: + Skipping command: blockid +at line 13, column (approximately) 11 (file position 176) +storing read block: TAXA +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/paup_characters.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/paup_characters.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/paup_characters.nex ] +Executing + +Warning: + Skipping command: blockid +at line 6, column (approximately) 13 (file position 188) +storing read block: TAXA +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/paup_characters.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/kim.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/kim.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/avian_ovomucoids.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/kim.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/kim.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/kim.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/avian_ovomucoids.nex +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/kim.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-dos.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-dos.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-dos.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-dos.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-dos.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-dos.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-rake.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-rake.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +storing read block: CODONS + +Warning: + An * is ignored in a CHARSET command +at line 67, column (approximately) 46 (file position 929) + +Warning: + An * is ignored in a CHARSET command +at line 68, column (approximately) 42 (file position 968) +storing read block: ASSUMPTIONS +storing read block: ASSUMPTIONS +storing read block: MESQUITECHARMODELS +storing read block: MESQUITE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-rake.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-rake.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-rake.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +storing read block: CODONS +storing read block: SETS +storing read block: ASSUMPTIONS +storing read block: MESQUITECHARMODELS +storing read block: MESQUITE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-rake.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/mdata.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/mdata.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/mdata.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/mdata.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/mdata.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: SETS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/mdata.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/nhxtree.nex" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/nhxtree.nex ] Executing @@ -1189,190 +1373,18 @@ storing read block: SETS storing read block: SETS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/linktest.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex ] -Executing -storing read block: TAXA -storing read block: DISTANCES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/distances.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex ] -Executing -storing read block: TAXA -storing read block: DISTANCES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/distances.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex ] -Executing -storing read block: TAXA -storing read block: UNALIGNED -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/unaligned.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex ] -Executing -storing read block: TAXA -storing read block: UNALIGNED -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/unaligned.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/anolis.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/anolis.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-dos.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-dos.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/basic-bush-dos.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-dos.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-dos.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/basic-bush-dos.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/charsets.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/charsets.nex ] -Executing - -Warning: - Skipping command: blockid -at line 13, column (approximately) 11 (file position 176) -storing read block: TAXA -storing read block: CHARACTERS -storing read block: SETS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/charsets.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/charsets.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/charsets.nex ] -Executing - -Warning: - Skipping command: blockid -at line 6, column (approximately) 13 (file position 183) -storing read block: TAXA -storing read block: CHARACTERS -storing read block: SETS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/charsets.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/bglobin.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/bglobin.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/bglobin.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/bglobin.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/bglobin.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/bglobin.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock.nex ] -Executing - -Warning: - A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. -at line 3, column (approximately) 13 (file position 32) -storing implied block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/notaxablock.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex ] -Executing -storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/notaxablock.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/replicase.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/replicase.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/replicase.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/replicase.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/replicase.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/replicase.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/paup_characters.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/paup_characters.nex ] -Executing - -Warning: - Skipping command: blockid -at line 13, column (approximately) 11 (file position 176) -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/paup_characters.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/paup_characters.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/paup_characters.nex ] -Executing - -Warning: - Skipping command: blockid -at line 6, column (approximately) 13 (file position 188) -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/paup_characters.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/dzmissing_bug.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/dzmissing_bug.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: ASSUMPTIONS -storing read block: MACCLADE -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/dzmissing_bug.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/dzmissing_bug.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/dzmissing_bug.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: ASSUMPTIONS -storing read block: MACCLADE -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/dzmissing_bug.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex ] -Executing -storing read block: TAXA -storing read block: TAXA -storing read block: TAXAASSOCIATION -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/associates.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex ] -Executing -storing read block: TAXA -storing read block: TAXA -storing read block: TAXAASSOCIATION -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/associates.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/kim.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/kim.nex ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex ] Executing storing implied block: TAXA storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/kim.nex -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/kim.nex" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/kim.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/primates.nex +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/kim.nex +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidOut/primates.nex "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/parens_intree.tre" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/NTSValidIn/parens_intree.tre ] Executing @@ -1403,18 +1415,30 @@ storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/funkyValidOut/choke.tre /usr/bin/python ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] +Executing +storing implied block: TAXA +storing read block: DATA +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy ] Executing storing implied block: TAXA storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy ] Executing storing read block: TAXA storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylip_emboss.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylip_emboss.phy ] Executing @@ -1427,30 +1451,30 @@ storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylip_emboss.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] Executing storing implied block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/relaxedphyliptree_q.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy ] +storing read block: DATA +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy ] Executing storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/relaxedphyliptree_q.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy ] Executing storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/phyliptree_simple.phy +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy ] Executing storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/phyliptree_simple.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aarelaxedphylip_rana.phy ] Executing @@ -1463,30 +1487,18 @@ storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] -Executing -storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaphylipinterleaved_emboss.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaphylipinterleaved_emboss.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/dnarelaxedphylip_brana.phy +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_rana.phy +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/dnarelaxedphylip_brana.phy "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aafasta_twoprot.fas" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aafasta_twoprot.fas ] Executing @@ -1499,18 +1511,6 @@ storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aafasta_twoprot.fas -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln ] -Executing -storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot_undec.aln" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot_undec.aln ] Executing @@ -1523,21 +1523,33 @@ storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot_undec.aln -/usr/bin/python ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn -"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/aarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/aarelaxedphylip_rana.phy ] +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln ] Executing -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) +storing implied block: TAXA +storing read block: DATA +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidIn/aaaln_twoprot.aln +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20180827.c71b264/test/ExternalValidOut/aaaln_twoprot.aln +/usr/bin/python ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn "/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy ] Executing Error: Illegal state code "q" found when reading site 2 for taxon grylioMVZ175945 at line 12, column (approximately) 28 (and file position 20065) +"/build/libncl-2.1.21+git20180827.c71b264/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/aarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20180827.c71b264/test/ExternalInvalidIn/aarelaxedphylip_rana.phy ] +Executing +Error: + Sequence longer than 1976 found for taxon temporariaDMH84R1. The character "o" was found, and will be ignored. If the file position of this error corresponds to sequences for the next taxon in the matrix, then that is an indication that the sequences for taxon temporariaDMH84R1 are too short. +at line 3, column (approximately) 2 (and file position 2011) /usr/bin/python ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer -/nonexistent/first-build/.ncl_round_triprc does not exist. Test stepped skipped. +/nonexistent/second-build/.ncl_round_triprc does not exist. Test stepped skipped. make[4]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' make[3]: Leaving directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' Making check in ot-subtree @@ -1616,7 +1628,7 @@ make[2]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/ncl' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libncl.so.2.0.0 libncl.so.2 || { rm -f libncl.so.2 && ln -s libncl.so.2.0.0 libncl.so.2; }; }) libtool: install: (cd /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libncl.so.2.0.0 libncl.so || { rm -f libncl.so && ln -s libncl.so.2.0.0 libncl.so; }; }) @@ -1642,7 +1654,7 @@ make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/check-taxo-nodes' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/checktaxonnodes /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/checktaxonnodes make[4]: Nothing to be done for 'install-data-am'. @@ -1659,7 +1671,7 @@ make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/find-unsupported-edges' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/findunsupportededges /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/findunsupportededges make[4]: Nothing to be done for 'install-data-am'. @@ -1690,7 +1702,7 @@ make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/normalizer' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSnormalizer /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/NEXUSnormalizer libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu' @@ -1704,7 +1716,7 @@ make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-subtree' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/otsubtree /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/otsubtree make[4]: Nothing to be done for 'install-data-am'. @@ -1714,7 +1726,7 @@ make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/ot-tree-inspect' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/otTreeInspect /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/otTreeInspect make[4]: Nothing to be done for 'install-data-am'. @@ -1724,7 +1736,7 @@ make[3]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' make[4]: Entering directory '/build/libncl-2.1.21+git20180827.c71b264/example/outdeg1count' /bin/mkdir -p '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/outdeg1count /build/libncl-2.1.21+git20180827.c71b264/debian/tmp/usr/bin/outdeg1count make[4]: Nothing to be done for 'install-data-am'. @@ -1836,8 +1848,8 @@ dh_builddeb dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20180827.c71b264-2_i386.deb'. -dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb'. +dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20180827.c71b264-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libncl_2.1.21+git20180827.c71b264-2_i386.changes @@ -1845,12 +1857,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/58725/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/58725/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/17966 and its subdirectories -I: Current time: Fri Mar 13 23:11:05 -12 2020 -I: pbuilder-time-stamp: 1584184265 +I: removing directory /srv/workspace/pbuilder/58725 and its subdirectories +I: Current time: Sat Apr 17 07:36:54 +14 2021 +I: pbuilder-time-stamp: 1618594614