Diff of the two buildlogs: -- --- b1/build.log 2023-05-21 09:43:47.996881988 +0000 +++ b2/build.log 2023-05-21 10:32:20.021163227 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 20 21:32:06 -12 2023 -I: pbuilder-time-stamp: 1684661526 +I: Current time: Sun May 21 23:44:14 +14 2023 +I: pbuilder-time-stamp: 1684662254 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./libncl_2.1.21+git20210811.b1213a7.orig.tar.xz] I: copying [./libncl_2.1.21+git20210811.b1213a7-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Jan 14 03:03:14 2023 -12 +gpgv: Signature made Sun Jan 15 05:03:14 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,167 @@ dpkg-source: info: applying python3.11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/16750/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14192/tmp/hooks/D01_modify_environment starting +debug: Running on virt32b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 21 23:45 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/14192/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14192/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='207fb6c7727d44c2aec85c0b6dfe32a1' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='16750' - PS1='# ' - PS2='> ' + INVOCATION_ID=810bf04089054d59b57dc1adf0a30b20 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=14192 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.cp9fBVB6/pbuilderrc_BmfS --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cp9fBVB6/b1 --logfile b1/build.log libncl_2.1.21+git20210811.b1213a7-4.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.cp9fBVB6/pbuilderrc_ZViT --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cp9fBVB6/b2 --logfile b2/build.log --extrapackages usrmerge libncl_2.1.21+git20210811.b1213a7-4.dsc' + SUDO_GID=112 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64b 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/16750/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 21 23:45 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/14192/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -242,7 +274,7 @@ Get: 40 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] -Fetched 23.2 MB in 2s (11.5 MB/s) +Fetched 23.2 MB in 2s (11.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19329 files and directories currently installed.) @@ -426,8 +458,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libncl_2.1.21+git20210811.b1213a7-4_source.changes +I: user script /srv/workspace/pbuilder/14192/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/14192/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libncl_2.1.21+git20210811.b1213a7-4_source.changes dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20210811.b1213a7-4 dpkg-buildpackage: info: source distribution unstable @@ -483,13 +526,13 @@ ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-constfuncs=yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking 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... arm-unknown-linux-gnueabihf @@ -507,10 +550,10 @@ checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -530,8 +573,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes @@ -577,7 +620,7 @@ checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C++ compiler works... yes -checking for egrep... (cached) /bin/grep -E +checking for egrep... (cached) /usr/bin/grep -E checking for float.h... yes checking for stdlib.h... (cached) yes checking for _Bool... no @@ -624,18 +667,20 @@ config.status: executing libtool commands make[1]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7' make all-recursive make[2]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7' Making all in ncl make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/ncl' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsassumptionsblock.lo nxsassumptionsblock.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsblock.lo nxsblock.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscharactersblock.lo nxscharactersblock.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -fPIC -DPIC -o .libs/nxsblock.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsassumptionsblock.lo nxsassumptionsblock.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsblock.lo nxsblock.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscharactersblock.lo nxscharactersblock.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscxxdiscretematrix.lo nxscxxdiscretematrix.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -fPIC -DPIC -o .libs/nxscxxdiscretematrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsassumptionsblock.cpp -fPIC -DPIC -o .libs/nxsassumptionsblock.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -fPIC -DPIC -o .libs/nxsblock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from nxsblock.cpp:21: @@ -657,15 +702,18 @@ from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, - from nxscharactersblock.cpp:26: + from ../ncl/nxscxxdiscretematrix.h:28, + from nxscxxdiscretematrix.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from nxscharactersblock.cpp:23: + from /usr/include/c++/12/streambuf:41, + from /usr/include/c++/12/bits/streambuf_iterator.h:35, + from /usr/include/c++/12/iterator:66, + from nxscxxdiscretematrix.cpp:19: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -684,6 +732,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from ../ncl/nxsexception.h:23, + from ../ncl/nxsblock.h:24, + from ../ncl/nxstaxablock.h:23, + from ../ncl/nxscharactersblock.h:29, + from nxscharactersblock.cpp:26: +../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/iomanip:40, + from nxscharactersblock.cpp:23: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:63, from ../ncl/nxsdefs.h:23: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': @@ -704,6 +768,12 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from ../ncl/nxscxxdiscretematrix.h:25: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const NxsCharacterPattern&}; _Tp = NxsCharacterPattern; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, @@ -729,77 +799,63 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = NxsCharacterPattern; _Alloc = std::allocator]', + inlined from 'void NxsConsumePatternSetToPatternVector(std::set&, std::vector&, const std::vector*, std::vector*, std::vector >*)' at nxscxxdiscretematrix.cpp:84:45: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxscxxdiscretematrix.lo nxscxxdiscretematrix.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -fPIC -DPIC -o .libs/nxscxxdiscretematrix.o +In file included from /usr/include/c++/12/map:60, + from ../ncl/nxsdefs.h:24, + from ../ncl/nxscxxdiscretematrix.h:26: +/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]': +/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::less, std::allocator >::const_iterator' changed in GCC 7.1 + 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdatablock.lo nxsdatablock.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, - from ../ncl/nxscxxdiscretematrix.h:28, - from nxscxxdiscretematrix.cpp:20: + from ../ncl/nxsdatablock.h:23, + from nxsdatablock.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/streambuf:41, - from /usr/include/c++/12/bits/streambuf_iterator.h:35, - from /usr/include/c++/12/iterator:66, - from nxscxxdiscretematrix.cpp:19: + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from ../ncl/nxscharactersblock.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from ../ncl/nxscxxdiscretematrix.h:25: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const NxsCharacterPattern&}; _Tp = NxsCharacterPattern; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = NxsCharacterPattern; _Alloc = std::allocator]', - inlined from 'void NxsConsumePatternSetToPatternVector(std::set&, std::vector&, const std::vector*, std::vector*, std::vector >*)' at nxscxxdiscretematrix.cpp:84:45: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from ../ncl/nxsdefs.h:24, - from ../ncl/nxscxxdiscretematrix.h:26: -/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]': -/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::less, std::allocator >::const_iterator' changed in GCC 7.1 - 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdistancesblock.lo nxsdistancesblock.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o +In file included from ../ncl/nxsexception.h:23, + from ../ncl/nxsblock.h:24, + from ../ncl/nxstaxablock.h:23, + from ../ncl/nxsdistancesblock.h:24, + from nxsdistancesblock.cpp:23: +../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/iomanip:40, + from nxsdistancesblock.cpp:19: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:63, from ../ncl/nxsdefs.h:23, from ../ncl/nxscharactersblock.h:27: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector NxsTransformationManager::GetDoubleWeights(const std::string&) const' at nxscharactersblock.cpp:1425:14: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool NxsCharactersBlock::HandleNextContinuousState(NxsToken&, unsigned int, unsigned int, ContinuousCharRow&, const NxsString&)' at nxscharactersblock.cpp:3019:31: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool NxsCharactersBlock::HandleNextContinuousState(NxsToken&, unsigned int, unsigned int, ContinuousCharRow&, const NxsString&)' at nxscharactersblock.cpp:3030:32: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:63, - from ../ncl/nxsassumptionsblock.h:23: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, @@ -832,29 +888,27 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdatablock.lo nxsdatablock.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o -In file included from ../ncl/nxsexception.h:23, - from ../ncl/nxsblock.h:24, - from ../ncl/nxstaxablock.h:23, - from ../ncl/nxscharactersblock.h:29, - from ../ncl/nxsdatablock.h:23, - from nxsdatablock.cpp:20: -../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 266 | : public std::binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from ../ncl/nxscharactersblock.h:23: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:63: +In file included from /usr/include/c++/12/vector:70, + from ../ncl/nxsdefs.h:23, + from ../ncl/nxscharactersblock.h:27: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector NxsTransformationManager::GetDoubleWeights(const std::string&) const' at nxscharactersblock.cpp:1425:14: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:63, + from ../ncl/nxsdefs.h:23, + from ../ncl/nxsdistancesblock.h:23: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, @@ -865,8 +919,7 @@ inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:316:21, - inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:286:22: + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:316:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -882,14 +935,13 @@ inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1934:18, inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:882:26, inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:137:7, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:320:17, - inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:286:22: + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:320:17: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 In file included from /usr/include/c++/12/vector:63, - from ../ncl/nxsdefs.h:23, - from ../ncl/nxscharactersblock.h:27: + from ../ncl/nxsassumptionsblock.h:23: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, @@ -922,40 +974,44 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsdistancesblock.lo nxsdistancesblock.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool NxsCharactersBlock::HandleNextContinuousState(NxsToken&, unsigned int, unsigned int, ContinuousCharRow&, const NxsString&)' at nxscharactersblock.cpp:3019:31: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool NxsCharactersBlock::HandleNextContinuousState(NxsToken&, unsigned int, unsigned int, ContinuousCharRow&, const NxsString&)' at nxscharactersblock.cpp:3030:32: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsexception.lo nxsexception.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o In file included from ../ncl/nxsexception.h:23, - from ../ncl/nxsblock.h:24, - from ../ncl/nxstaxablock.h:23, - from ../ncl/nxsdistancesblock.h:24, - from nxsdistancesblock.cpp:23: + from nxsexception.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from nxsdistancesblock.cpp:19: +In file included from /usr/include/c++/12/functional:49, + from ../ncl/nxsstring.h:26: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:63, - from ../ncl/nxsdefs.h:23, - from ../ncl/nxsdistancesblock.h:23: +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsmultiformat.lo nxsmultiformat.cpp +In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -fPIC -DPIC -o .libs/nxsmultiformat.o In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:316:21: + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:316:21, + inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:286:22: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -971,28 +1027,12 @@ inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1934:18, inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:882:26, inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:137:7, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:320:17: + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:320:17, + inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:286:22: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsexception.lo nxsexception.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o -In file included from ../ncl/nxsexception.h:23, - from nxsexception.cpp:20: -../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 266 | : public std::binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/functional:49, - from ../ncl/nxsstring.h:26: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsmultiformat.lo nxsmultiformat.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -fPIC -DPIC -o .libs/nxsmultiformat.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxspublicblocks.lo nxspublicblocks.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, @@ -1011,6 +1051,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxspublicblocks.lo nxspublicblocks.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, @@ -1027,6 +1069,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 In file included from /usr/include/c++/12/vector:63, from ../ncl/nxspublicblocks.h:22: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': @@ -1072,9 +1115,9 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsreader.lo nxsreader.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsreader.lo nxsreader.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o In file included from ../ncl/nxsreader.h:24, from nxsreader.cpp:26: @@ -1087,8 +1130,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxssetreader.lo nxssetreader.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxssetreader.lo nxssetreader.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsstring.lo nxsstring.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -fPIC -DPIC -o .libs/nxsstring.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxstoken.h:23, from ../ncl/nxssetreader.h:23, @@ -1106,8 +1151,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsstring.lo nxsstring.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -fPIC -DPIC -o .libs/nxsstring.o In file included from nxsstring.cpp:25: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function @@ -1123,13 +1166,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, @@ -1148,6 +1189,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, @@ -1235,10 +1278,8 @@ 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstoken.lo nxstoken.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstoken.lo nxstoken.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -fPIC -DPIC -o .libs/nxstoken.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxstoken.h:23, from nxstoken.cpp:22: @@ -1255,6 +1296,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, @@ -1280,27 +1323,7 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from ../ncl/nxsdefs.h:24, - from ../ncl/nxstreesblock.h:24: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ProcessedNxsToken}; _Tp = ProcessedNxsToken; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'static std::vector NxsToken::Tokenize(const std::string&)' at nxstoken.cpp:388:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ProcessedNxsToken}; _Tp = ProcessedNxsToken; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void NxsToken::ProcessAsCommand(ProcessedNxsCommand*)' at nxstoken.cpp:406:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, @@ -1321,12 +1344,67 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ProcessedNxsToken}; _Tp = ProcessedNxsToken; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'static std::vector NxsToken::Tokenize(const std::string&)' at nxstoken.cpp:388:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ProcessedNxsToken}; _Tp = ProcessedNxsToken; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void NxsToken::ProcessAsCommand(ProcessedNxsCommand*)' at nxstoken.cpp:406:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:60, + from ../ncl/nxsdefs.h:24, + from ../ncl/nxstreesblock.h:24: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1 In file included from /usr/include/c++/12/vector:70, from ../ncl/nxsdefs.h:23: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {NxsFullTreeDescription}; _Tp = NxsFullTreeDescription; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:63, + from ../ncl/nxsdefs.h:23: +/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': +/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, + inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:316:21, + inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:286:22: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/12/bits/new_allocator.h:175:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:713:33, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:2005:32, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1321:19, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1934:18, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:882:26, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:137:7, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:320:17, + inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:286:22: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -o nxsunalignedblock.o >/dev/null 2>&1 In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::vector > NxsSimpleTree::GetDblPathDistances(bool) const' at nxstreesblock.cpp:466:22: @@ -1429,43 +1507,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:63, - from ../ncl/nxsdefs.h:23: -/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': -/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, - inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:316:21, - inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:286:22: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/12/bits/new_allocator.h:175:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, - inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:713:33, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:2005:32, - inlined from 'std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1321:19, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1934:18, - inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:882:26, - inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:137:7, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:320:17, - inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:286:22: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -o nxsunalignedblock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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/arm-linux-gnueabihf 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+git20210811.b1213a7=. -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/arm-linux-gnueabihf 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/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/12/crtbeginS.o .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxscxxdiscretematrix.o .libs/nxsdatablock.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsmultiformat.o .libs/nxspublicblocks.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstaxaassociationblock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -L/usr/lib/gcc/arm-linux-gnueabihf/12 -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/12/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -O3 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0 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") @@ -1525,7 +1568,7 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/basiccmdline' Making all in check-taxo-nodes @@ -1546,7 +1589,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/check-taxo-nodes' Making all in compressor @@ -1566,7 +1609,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/compressor' Making all in find-unsupported-edges @@ -1587,7 +1630,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/find-unsupported-edges' Making all in gapcode @@ -1620,7 +1663,7 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/gapcode' Making all in nclsimplest @@ -1641,7 +1684,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/nclsimplest' Making all in ncltest @@ -1694,7 +1737,7 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/ncltest' Making all in normalizer @@ -1702,11 +1745,7 @@ 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+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o normalizer.o normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_VALIDATE_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSvalidator-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp -In file included from ../../ncl/ncl.h:79, - from normalizer.cpp:46: -../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 266 | : public std::binary_function - | ^~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1722,6 +1761,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from ../../ncl/ncl.h:79, + from us2ml.cpp:22: +../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::binary_function + | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, @@ -1747,11 +1791,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, - from us2ml.cpp:22: + from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ @@ -1765,6 +1806,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, from converter.cpp:48: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1795,7 +1839,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1814,7 +1857,7 @@ 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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, - from normalizer.cpp:46: + from us2ml.cpp:22: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ @@ -1829,7 +1872,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, - from us2ml.cpp:22: + from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ @@ -1843,17 +1886,17 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer' Making all in ot-subtree @@ -1874,7 +1917,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/ot-subtree' Making all in ot-tree-inspect @@ -1895,7 +1938,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/ot-tree-inspect' Making all in outdeg1count @@ -1916,7 +1959,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/outdeg1count' Making all in patristic @@ -1969,7 +2012,7 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/patristic' Making all in phylobaseinterface @@ -2002,7 +2045,7 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/phylobaseinterface' Making all in polytomy-count @@ -2023,7 +2066,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/polytomy-count' Making all in splitsinfile @@ -2031,6 +2074,22 @@ 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+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUStosplits-splitsinfile.o `test -f 'splitsinfile.cpp' || echo './'`splitsinfile.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp +In file included from ../../ncl/nxsexception.h:23, + from ../../ncl/nxsblock.h:24, + from ../../ncl/nxstaxablock.h:23, + from ../../ncl/nxstreesblock.h:25, + from splitsstructs.h:9, + from splitsstructs.cpp:1: +../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from splitsstructs.h:3: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from ../../ncl/nxsexception.h:23, from ../../ncl/nxsblock.h:24, from ../../ncl/nxstaxablock.h:23, @@ -2090,41 +2149,17 @@ /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void TreesToSplits::recordSplit(const Split&, const NxsSimpleNode*, SplitsMap&, unsigned int)' at splitsstructs.cpp:141:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void TreesToSplits::recordTreeToSplitsMap(const NxsFullTreeDescription&, SplitsMap&, unsigned int)' at splitsstructs.cpp:63:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp -In file included from ../../ncl/nxsexception.h:23, - from ../../ncl/nxsblock.h:24, - from ../../ncl/nxstaxablock.h:23, - from ../../ncl/nxstreesblock.h:25, - from splitsstructs.h:9, - from splitsstructs.cpp:1: -../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 266 | : public std::binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from splitsstructs.h:3: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/map:60, @@ -2146,7 +2181,15 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void TreesToSplits::recordTreeToSplitsMap(const NxsFullTreeDescription&, SplitsMap&, unsigned int)' at splitsstructs.cpp:63:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/splitsinfile' Making all in subsetter @@ -2165,7 +2208,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/subsetter' Making all in translate @@ -2229,7 +2272,7 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libncl-2.1.21+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7=. -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+git20210811.b1213a7/example/translate' make[4]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example' @@ -2245,7 +2288,7 @@ make[2]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7' make[1]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7' dh_auto_test - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7' Making check in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/ncl' @@ -2339,46 +2382,90 @@ storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/data/sample.tre /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex ] +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex ] Executing - -Warning: - Skipping command: blockid -at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS -storing read block: TREES -storing read block: SETS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex ] +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex ] Executing Warning: - Skipping command: blockid -at line 6, column (approximately) 13 (file position 183) + 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+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex ] +Executing storing read block: TAXA -storing read block: CHARACTERS storing read block: TREES -storing read block: SETS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/m.nex" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/m.nex ] Executing @@ -2393,34 +2480,52 @@ storing read block: CHARACTERS storing read block: SETS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/m.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex ] +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex ] Executing storing read block: TAXA -storing read block: UNALIGNED -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex ] +storing read block: CHARACTERS +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex ] Executing storing read block: TAXA -storing read block: UNALIGNED -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex ] +storing read block: TAXA +storing read block: TAXAASSOCIATION +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex ] Executing storing read block: TAXA -storing read block: CHARACTERS +storing read block: TAXA +storing read block: TAXAASSOCIATION +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex ] +Executing + +Warning: + A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. +at line 3, column (approximately) 10 (file position 26) +storing implied block: TAXA storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex ] Executing storing read block: TAXA -storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex ] Executing Warning: @@ -2428,14 +2533,46 @@ 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+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex ] +Executing + +Warning: + Skipping command: blockid +at line 6, column (approximately) 13 (file position 188) +storing read block: TAXA storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex ] +Executing +storing read block: TAXA storing read block: CHARACTERS +storing read block: SETS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex ] +Executing + +Warning: + Skipping command: blockid +at line 13, column (approximately) 11 (file position 176) +storing read block: TAXA storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex ] +storing read block: TREES +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex ] Executing Warning: @@ -2443,12 +2580,88 @@ at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS +storing read block: TREES +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: ASSUMPTIONS +storing read block: MACCLADE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex ] +Executing +storing read block: TAXA storing read block: CHARACTERS +storing read block: ASSUMPTIONS +storing read block: MACCLADE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex ] +Executing + +Warning: + Skipping command: blockid +at line 13, column (approximately) 11 (file position 189) +storing read block: TAXA + +Warning: + Skipping command: blockid +at line 27, column (approximately) 11 (file position 388) +storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS + +Warning: + Skipping unknown LINK subcommand: characters +at line 61, column (approximately) 38 (file position 1551) +storing read block: TREES + +Warning: + Skipping unknown LINK subcommand: characters +at line 71, column (approximately) 38 (file position 1745) +storing read block: TREES +storing implied block: ASSUMPTIONS +storing implied block: ASSUMPTIONS +storing read block: ASSUMPTIONS + +Warning: + A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s). +at line 90, column (approximately) 42 (file position 2360) +storing read block: ASSUMPTIONS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex ] +Executing + +Warning: + Skipping command: blockid +at line 6, column (approximately) 13 (file position 168) +storing read block: TAXA + +Warning: + Skipping command: blockid +at line 12, column (approximately) 13 (file position 341) +storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex +storing read block: TREES +storing read block: TREES +storing read block: SETS +storing read block: SETS +storing read block: SETS + +Warning: + A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s). +at line 84, column (approximately) 20 (file position 2384) +storing read block: SETS +storing read block: SETS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/charsets.nex" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/charsets.nex ] Executing @@ -2487,52 +2700,94 @@ storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/adh.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex ] +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex ] +Executing +storing read block: TAXA +storing read block: UNALIGNED +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex ] +Executing +storing read block: TAXA +storing read block: UNALIGNED +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex ] +storing read block: CODONS + +Warning: + An * is ignored in a CHARSET command +at line 67, column (approximately) 46 (file position 1014) + +Warning: + An * is ignored in a CHARSET command +at line 68, column (approximately) 42 (file position 1053) +storing read block: ASSUMPTIONS +storing read block: ASSUMPTIONS +storing read block: MESQUITECHARMODELS +storing read block: MESQUITE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex ] +storing read block: CODONS +storing read block: SETS +storing read block: ASSUMPTIONS +storing read block: MESQUITECHARMODELS +storing read block: MESQUITE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex ] Executing -storing implied block: TAXA -storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex ] +storing read block: TAXA +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. -at line 3, column (approximately) 13 (file position 32) +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+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex ] Executing storing read block: TAXA storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex ] Executing Warning: @@ -2540,17 +2795,27 @@ 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+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex ] +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex ] Executing Warning: Skipping command: blockid -at line 6, column (approximately) 13 (file position 188) +at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex ] Executing @@ -2599,136 +2864,48 @@ storing read block: MESQUITECHARMODELS storing read block: MESQUITE ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-rake.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex ] -Executing - -Warning: - A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. -at line 3, column (approximately) 10 (file position 26) -storing implied block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex ] -Executing -storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: SETS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex ] +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -storing read block: CODONS - -Warning: - An * is ignored in a CHARSET command -at line 67, column (approximately) 46 (file position 1014) - -Warning: - An * is ignored in a CHARSET command -at line 68, column (approximately) 42 (file position 1053) -storing read block: ASSUMPTIONS -storing read block: ASSUMPTIONS -storing read block: MESQUITECHARMODELS -storing read block: MESQUITE -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -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+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex ] Executing @@ -2741,154 +2918,20 @@ storing read block: TAXA storing read block: DISTANCES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/distances.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: ASSUMPTIONS -storing read block: MACCLADE -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: ASSUMPTIONS -storing read block: MACCLADE -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex ] -Executing - -Warning: - A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. -at line 3, column (approximately) 7 (file position 26) -storing implied block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex ] -Executing -storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex ] -Executing -storing read block: TAXA -storing read block: TAXA -storing read block: TAXAASSOCIATION -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex ] -Executing -storing read block: TAXA -storing read block: TAXA -storing read block: TAXAASSOCIATION -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex ] +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex ] Executing - -Warning: - Skipping command: blockid -at line 13, column (approximately) 11 (file position 189) -storing read block: TAXA - -Warning: - Skipping command: blockid -at line 27, column (approximately) 11 (file position 388) storing read block: TAXA storing read block: CHARACTERS -storing read block: CHARACTERS - -Warning: - Skipping unknown LINK subcommand: characters -at line 61, column (approximately) 38 (file position 1551) storing read block: TREES - -Warning: - Skipping unknown LINK subcommand: characters -at line 71, column (approximately) 38 (file position 1745) -storing read block: TREES -storing implied block: ASSUMPTIONS -storing implied block: ASSUMPTIONS -storing read block: ASSUMPTIONS - -Warning: - A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s). -at line 90, column (approximately) 42 (file position 2360) -storing read block: ASSUMPTIONS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex ] Executing - -Warning: - Skipping command: blockid -at line 6, column (approximately) 13 (file position 168) -storing read block: TAXA - -Warning: - Skipping command: blockid -at line 12, column (approximately) 13 (file position 341) storing read block: TAXA storing read block: CHARACTERS -storing read block: CHARACTERS -storing read block: TREES storing read block: TREES -storing read block: SETS -storing read block: SETS -storing read block: SETS - -Warning: - A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s). -at line 84, column (approximately) 20 (file position 2384) -storing read block: SETS -storing read block: SETS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre ] Executing @@ -2919,30 +2962,42 @@ storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/funkyValidOut/choke.tre /usr/bin/python3 ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy ] +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy ] +Executing +storing implied block: TAXA +storing read block: DATA +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/relaxedphyliptree_q.phy" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/relaxedphyliptree_q.phy ] Executing @@ -2955,30 +3010,6 @@ storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/relaxedphyliptree_q.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] -Executing -storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy ] -Executing -storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/phyliptree_simple.phy" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/phyliptree_simple.phy ] Executing @@ -2991,42 +3022,42 @@ storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/phyliptree_simple.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln -"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot.aln" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot.aln ] Executing @@ -3039,6 +3070,18 @@ storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot.aln +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln ] +Executing +storing implied block: TAXA +storing read block: DATA +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln +"/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln /usr/bin/python3 ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn "/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/aarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/aarelaxedphylip_rana.phy ] @@ -3093,13 +3136,6 @@ make check-local make[4]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/translate' /usr/bin/python3 ../../test/roundTripNCLTest.py -o ../../example/translate/NEXUStranslate ../../test/TranslateIn ../../test/TranslateOut -"/build/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex" -[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: CODONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex "/build/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex" [Reading /build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex ] Executing @@ -3107,6 +3143,13 @@ storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex +"/build/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate" "-s2" "/build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex" +[Reading /build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex ] +Executing +storing implied block: TAXA +storing read block: DATA +storing read block: CODONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate succeeded for /build/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex make[4]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7/example/translate' make[3]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7/example/translate' make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example' @@ -3128,8 +3171,8 @@ Making install in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/ncl' make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/ncl' - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf' - /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf' + /bin/sh ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.so.2.0.0 libtool: install: (cd /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libncl.so.2.0.0 libncl.so.2 || { rm -f libncl.so.2 && ln -s libncl.so.2.0.0 libncl.so.2; }; }) libtool: install: (cd /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libncl.so.2.0.0 libncl.so || { rm -f libncl.so && ln -s libncl.so.2.0.0 libncl.so; }; }) @@ -3138,7 +3181,7 @@ libtool: install: chmod 644 /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.a libtool: install: ranlib /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/include/ncl' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/include/ncl' /usr/bin/install -c -m 644 ncl.h nxsallocatematrix.h nxsassumptionsblock.h nxsblock.cpp nxsblock.h nxscharactersblock.h nxscdiscretematrix.h nxscxxdiscretematrix.h nxsdatablock.h nxsdefs.h nxsdiscretedatum.h nxsdistancedatum.h nxsdistancesblock.h nxsexception.h nxsmultiformat.h nxspublicblocks.h nxsreader.h nxssetreader.h nxsstring.h nxstaxablock.h nxstaxaassociationblock.h nxstoken.h nxstreesblock.h nxsunalignedblock.h nxsutilcopy.h '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/include/ncl' make[3]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7/ncl' make[2]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7/ncl' @@ -3154,8 +3197,8 @@ Making install in check-taxo-nodes make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' make[4]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/checktaxonnodes /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/checktaxonnodes make[4]: Nothing to be done for 'install-data-am'. @@ -3171,8 +3214,8 @@ Making install in find-unsupported-edges make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' make[4]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/findunsupportededges /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/findunsupportededges make[4]: Nothing to be done for 'install-data-am'. @@ -3202,8 +3245,8 @@ Making install in normalizer make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer' make[4]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/normalizer' - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/NEXUSnormalizer /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/NEXUSnormalizer libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' @@ -3216,8 +3259,8 @@ Making install in ot-subtree make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' make[4]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/otsubtree /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/otsubtree make[4]: Nothing to be done for 'install-data-am'. @@ -3226,8 +3269,8 @@ Making install in ot-tree-inspect make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' make[4]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/otTreeInspect /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/otTreeInspect make[4]: Nothing to be done for 'install-data-am'. @@ -3236,8 +3279,8 @@ Making install in outdeg1count make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' make[4]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/outdeg1count /build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/outdeg1count make[4]: Nothing to be done for 'install-data-am'. @@ -3302,7 +3345,7 @@ make[2]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7' make[3]: Entering directory '/build/libncl-2.1.21+git20210811.b1213a7' make[3]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 nclv2.1.pc '/build/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' make[3]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7' make[2]: Leaving directory '/build/libncl-2.1.21+git20210811.b1213a7' @@ -3346,15 +3389,15 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/NEXUSnormalizer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/checktaxonnodes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/findunsupportededges contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libncl2/usr/lib/arm-linux-gnueabihf/libncl.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/otTreeInspect contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/otsubtree contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/NCLconverter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/findunsupportededges contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/NEXUSnormalizer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/NEXUSvalidator contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/checktaxonnodes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/otsubtree contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/ncl-tools/usr/bin/outdeg1count contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libncl2/usr/lib/arm-linux-gnueabihf/libncl.so.2.0.0 found in none of the libraries dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libncl-dev: substitution variable ${shlibs:Depends} used, but is not defined @@ -3372,12 +3415,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/14192/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14192/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/16750 and its subdirectories -I: Current time: Sat May 20 21:43:44 -12 2023 -I: pbuilder-time-stamp: 1684662224 +I: removing directory /srv/workspace/pbuilder/14192 and its subdirectories +I: Current time: Mon May 22 00:32:15 +14 2023 +I: pbuilder-time-stamp: 1684665135