Diff of the two buildlogs: -- --- b1/build.log 2021-08-11 20:12:14.482904470 +0000 +++ b2/build.log 2021-08-11 20:32:05.446379575 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 11 07:54:49 -12 2021 -I: pbuilder-time-stamp: 1628711689 +I: Current time: Thu Aug 12 10:12:41 +14 2021 +I: pbuilder-time-stamp: 1628712761 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./libncl_2.1.21+git20190531.feceb81-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.JtJ75LVk/trustedkeys.kbx': General error -gpgv: Signature made Thu Jul 23 01:04:01 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.6xI4NEx_/trustedkeys.kbx': General error +gpgv: Signature made Fri Jul 24 03:04:01 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6296/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/18094/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/18094/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/18094/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,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='52715cf0027f44b5964045404b56be34' - 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='6296' - PS1='# ' - PS2='> ' + INVOCATION_ID=c46a1bd00f6f4e1aad701a0328f2eac1 + 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=18094 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/tmp.Vou8RLBIzA/pbuilderrc_wsss --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Vou8RLBIzA/b1 --logfile b1/build.log libncl_2.1.21+git20190531.feceb81-3.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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/tmp.Vou8RLBIzA/pbuilderrc_XM5K --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Vou8RLBIzA/b2 --logfile b2/build.log --extrapackages usrmerge libncl_2.1.21+git20190531.feceb81-3.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux jtx1c 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 21:25 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/6296/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 12 10:13 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 10 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/18094/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -244,7 +278,7 @@ Get: 42 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] -Fetched 22.7 MB in 2s (10.6 MB/s) +Fetched 22.7 MB in 3s (8356 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) @@ -437,8 +471,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (697 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 22016 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/libncl-2.1.21+git20190531.feceb81/ && 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+git20190531.feceb81-3_source.changes +hostname: Name or service not known +I: Running cd /build/libncl-2.1.21+git20190531.feceb81/ && 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+git20190531.feceb81-3_source.changes dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20190531.feceb81-3 dpkg-buildpackage: info: source distribution unstable @@ -473,13 +544,13 @@ ./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 thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe 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 @@ -497,10 +568,10 @@ checking for gcc option to accept ISO C89... 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 @@ -519,8 +590,8 @@ 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 how to run the C preprocessor... gcc -E @@ -618,21 +689,20 @@ config.status: executing libtool commands make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' make all-recursive make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' Making all in ncl make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -fPIC -DPIC -o .libs/nxsblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o In file included from /usr/include/c++/10/vector:72, from ../ncl/nxscxxdiscretematrix.h:25, from nxscxxdiscretematrix.cpp:20: @@ -647,6 +717,7 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1 In file included from /usr/include/c++/10/map:60, from ../ncl/nxsdefs.h:24, from ../ncl/nxscxxdiscretematrix.h:26, @@ -656,6 +727,11 @@ 2193 | _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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 In file included from /usr/include/c++/10/vector:72, from ../ncl/nxsdefs.h:23, from ../ncl/nxscharactersblock.h:27, @@ -680,8 +756,9 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o In file included from /usr/include/c++/10/vector:67, from ../ncl/nxsdefs.h:23, from ../ncl/nxscharactersblock.h:27, @@ -693,39 +770,33 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxspublicblocks.lo nxspublicblocks.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsstring.lo nxsstring.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -fPIC -DPIC -o .libs/nxsstring.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxaassociationblock.cpp -o nxstaxaassociationblock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o In file included from /usr/include/c++/10/vector:72, from ../ncl/nxsdefs.h:23, @@ -745,6 +816,7 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp In file included from /usr/include/c++/10/map:60, from ../ncl/nxsdefs.h:24, from ../ncl/nxstreesblock.h:24, @@ -753,9 +825,8 @@ /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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++/10/map:61, from ../ncl/nxsdefs.h:24, from ../ncl/nxstreesblock.h:24, @@ -821,7 +892,7 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxsunalignedblock.cpp -o nxsunalignedblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/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/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../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") @@ -834,25 +905,25 @@ Making all in basiccmdline make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/basiccmdline' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o basiccmdline.o basiccmdline.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/basiccmdline' Making all in check-taxo-nodes make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o checktaxonnodes-checktaxonnodes.o `test -f 'checktaxonnodes.cpp' || echo './'`checktaxonnodes.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/check-taxo-nodes' Making all in compressor make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/compressor' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSCharacterCompressor-compressor.o `test -f 'compressor.cpp' || echo './'`compressor.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/compressor' Making all in find-unsupported-edges make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o findunsupportededges-findunsupportededges.o `test -f 'findunsupportededges.cpp' || echo './'`findunsupportededges.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/find-unsupported-edges' Making all in gapcode @@ -872,19 +943,19 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/gapcode' Making all in nclsimplest make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/nclsimplest' g++ -DHAVE_CONFIG_H -I. -I../.. -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o nclsimplest.o nclsimplest.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/nclsimplest' Making all in ncltest make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ncltest' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o ncltest.o ncltest.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/ncltest' Making all in normalizer @@ -898,41 +969,41 @@ 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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/normalizer' Making all in ot-subtree make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otsubtree-otsubtree.o `test -f 'otsubtree.cpp' || echo './'`otsubtree.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/ot-subtree' Making all in ot-tree-inspect make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o otTreeInspect-ot_tree_inspect.o `test -f 'ot_tree_inspect.cpp' || echo './'`ot_tree_inspect.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/ot-tree-inspect' Making all in outdeg1count make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o outdeg1count-outdeg1count.o `test -f 'outdeg1count.cpp' || echo './'`outdeg1count.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/outdeg1count' Making all in patristic make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/patristic' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o patristic.o patristic.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/patristic' Making all in phylobaseinterface @@ -949,13 +1020,13 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/phylobaseinterface' Making all in polytomy-count make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/polytomy-count' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o polytomycount-polytomy_count.o `test -f 'polytomy_count.cpp' || echo './'`polytomy_count.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/polytomy-count' Making all in splitsinfile @@ -963,6 +1034,7 @@ 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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp In file included from /usr/include/c++/10/vector:72, from splitsstructs.h:3, from splitsstructs.cpp:1: @@ -980,23 +1052,6 @@ /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from splitsstructs.h:3, - from splitsstructs.cpp:1: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void TreesToSplits::recordSplit(const Split&, const NxsSimpleNode*, TreesToSplits::SplitsMap&, unsigned int)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from splitsstructs.h:3, - from splitsstructs.cpp:1: -/usr/include/c++/10/bits/vector.tcc: In member function 'void TreesToSplits::recordTreeToSplitsMap(const NxsFullTreeDescription&, TreesToSplits::SplitsMap&, unsigned int)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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++/10/vector:72, from splitsstructs.h:3, from splitsstructs.cpp:1: @@ -1006,6 +1061,13 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:67, + from splitsstructs.h:3, + from splitsstructs.cpp:1: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void TreesToSplits::recordSplit(const Split&, const NxsSimpleNode*, TreesToSplits::SplitsMap&, unsigned int)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from ../../ncl/nxsdefs.h:24, from splitsstructs.h:8, @@ -1028,13 +1090,22 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 file included from /usr/include/c++/10/vector:72, + from splitsstructs.h:3, + from splitsstructs.cpp:1: +/usr/include/c++/10/bits/vector.tcc: In member function 'void TreesToSplits::recordTreeToSplitsMap(const NxsFullTreeDescription&, TreesToSplits::SplitsMap&, unsigned int)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/splitsinfile' Making all in subsetter make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/subsetter' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -ffast-math -c -o NEXUSsubsetter-subsetter.o `test -f 'subsetter.cpp' || echo './'`subsetter.cpp -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/subsetter' Making all in translate @@ -1054,7 +1125,7 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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 -fdebug-prefix-map=/build/libncl-2.1.21+git20190531.feceb81=. -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+git20190531.feceb81/example/translate' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example' @@ -1070,7 +1141,7 @@ make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' make[1]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' dh_auto_test - make -j3 check VERBOSE=1 + make -j4 check VERBOSE=1 make[1]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' Making check in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' @@ -1176,66 +1247,98 @@ storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/data/sample.tre /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex ] +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex ] Executing -storing read block: TAXA -storing read block: UNALIGNED +storing implied block: TAXA +storing read block: DATA +storing read block: ASSUMPTIONS +storing read block: MACCLADE /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:106: DeprecationWarning: 'U' mode is deprecated e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex ] Executing storing read block: TAXA -storing read block: UNALIGNED -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex ] +storing read block: CHARACTERS +storing read block: ASSUMPTIONS +storing read block: MACCLADE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex ] Executing storing implied block: TAXA storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex ] +storing read block: CODONS + +Warning: + An * is ignored in a CHARSET command +at line 67, column (approximately) 46 (file position 929) + +Warning: + An * is ignored in a CHARSET command +at line 68, column (approximately) 42 (file position 968) +storing read block: ASSUMPTIONS +storing read block: ASSUMPTIONS +storing read block: MESQUITECHARMODELS +storing read block: MESQUITE +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mac.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mac.nex ] Executing @@ -1250,20 +1353,144 @@ storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mac.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex ] +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex ] +Executing + +Warning: + Skipping command: blockid +at line 13, column (approximately) 11 (file position 176) +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex ] +Executing + +Warning: + Skipping command: blockid +at line 6, column (approximately) 13 (file position 183) +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex ] +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/cynmix.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/cynmix.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex ] +Executing +storing read block: TAXA +storing read block: CHARACTERS +storing read block: SETS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex ] +Executing +storing read block: TAXA +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/t.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/t.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex ] +Executing + +Warning: + Skipping command: blockid +at line 13, column (approximately) 11 (file position 176) +storing read block: TAXA +storing read block: CHARACTERS +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex ] +Executing + +Warning: + Skipping command: blockid +at line 6, column (approximately) 13 (file position 183) +storing read block: TAXA +storing read block: CHARACTERS +storing read block: SETS +storing read block: ASSUMPTIONS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/characters.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/characters.nex ] Executing @@ -1294,118 +1521,138 @@ storing read block: CHARACTERS storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/characters.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex ] +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex ] -Executing + Skipping command: blockid +at line 13, column (approximately) 11 (file position 176) storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex ] Executing + +Warning: + Skipping command: blockid +at line 6, column (approximately) 13 (file position 188) storing read block: TAXA storing read block: CHARACTERS -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-mixed-line-endings.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-mixed-line-endings.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex ] -Executing -storing implied block: TAXA -storing read block: DATA -storing read block: MRBAYES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/adh.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/adh.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex ] Executing -storing implied block: TAXA -storing read block: DATA -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/mdata.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex ] +storing read block: TAXA +storing read block: CHARACTERS +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -storing read block: SETS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/mdata.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex ] +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/replicase.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/replicase.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/avian_ovomucoids.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/anolis.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/avian_ovomucoids.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/anolis.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/treeswithouttaxa.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-unix.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/treeswithouttaxa.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex ] +Executing + +Warning: + A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. +at line 3, column (approximately) 13 (file position 32) +storing implied block: TAXA +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex ] Executing storing read block: TAXA -storing read block: CHARACTERS storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-unix.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex ] +Executing +storing read block: TAXA +storing read block: UNALIGNED +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/unaligned.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex ] +Executing +storing read block: TAXA +storing read block: UNALIGNED +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/unaligned.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/primates.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex ] +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/bglobin.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/primates.nex +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/bglobin.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/associates.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/associates.nex ] Executing @@ -1420,64 +1667,32 @@ storing read block: TAXA storing read block: TAXAASSOCIATION ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/associates.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex ] +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/partitions.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex ] +storing implied block: TAXA +storing read block: DATA +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex ] Executing - -Warning: - Skipping command: blockid -at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS -storing read block: TREES -storing read block: SETS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/partitions.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex ] +storing read block: MRBAYES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex ] Executing storing read block: TAXA -storing read block: CHARACTERS -storing read block: TREES -storing read block: CODONS - -Warning: - An * is ignored in a CHARSET command -at line 67, column (approximately) 46 (file position 929) - -Warning: - An * is ignored in a CHARSET command -at line 68, column (approximately) 42 (file position 968) -storing read block: ASSUMPTIONS -storing read block: ASSUMPTIONS -storing read block: MESQUITECHARMODELS -storing read block: MESQUITE -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-rake.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex ] +storing read block: DISTANCES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-rake.nex +storing read block: DISTANCES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/linktest.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/linktest.nex ] Executing @@ -1540,18 +1755,6 @@ storing read block: SETS storing read block: SETS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/linktest.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex ] -Executing -storing read block: TAXA -storing read block: DISTANCES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/distances.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex ] -Executing -storing read block: TAXA -storing read block: DISTANCES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/distances.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-dos.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/basic-bush-dos.nex ] Executing @@ -1566,122 +1769,6 @@ storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/basic-bush-dos.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/dzmissing_bug.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/dzmissing_bug.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock-quotes.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex ] -Executing -storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock-quotes.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/m.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -storing read block: SETS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/m.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex ] -Executing - -Warning: - Skipping command: blockid -at line 13, column (approximately) 11 (file position 176) -storing read block: TAXA -storing read block: CHARACTERS -storing read block: SETS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/charsets.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex ] -Executing - -Warning: - Skipping command: blockid -at line 6, column (approximately) 13 (file position 183) -storing read block: TAXA -storing read block: CHARACTERS -storing read block: SETS -storing read block: ASSUMPTIONS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/charsets.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex ] -Executing - -Warning: - Skipping command: blockid -at line 13, column (approximately) 11 (file position 176) -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/paup_characters.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/paup_characters.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/kim.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/kim.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/protein.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/protein.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/nhxtree.nex" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/nhxtree.nex ] Executing @@ -1714,22 +1801,6 @@ storing read block: MESQUITECHARMODELS storing read block: MESQUITE ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/nhxtree.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex ] -Executing - -Warning: - A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. -at line 3, column (approximately) 13 (file position 32) -storing implied block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/notaxablock.nex -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex ] -Executing -storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidOut/notaxablock.nex "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/parens_intree.tre" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/NTSValidIn/parens_intree.tre ] Executing @@ -1764,8 +1835,8 @@ storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/funkyValidOut/choke.tre /usr/bin/python3 ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy ] +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] Executing storing implied block: TAXA storing read block: DATA @@ -1773,37 +1844,37 @@ e = open(expectedOut, "rU") /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/../../test/roundTripNCLTest.py:107: DeprecationWarning: 'U' mode is deprecated o = open(tf, "rU") -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_brana.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylip_emboss.phy +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_brana.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylip_emboss.phy +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy ] +storing read block: DATA +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA -storing read block: TREES -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy +storing read block: CHARACTERS +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] Executing @@ -1816,30 +1887,18 @@ storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/dnarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy ] -Executing -storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy ] -Executing -storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy ] Executing storing implied block: TAXA -storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaphylipinterleaved_emboss.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/relaxedphyliptree_q.phy +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy ] Executing storing read block: TAXA -storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaphylipinterleaved_emboss.phy +storing read block: TREES +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/relaxedphyliptree_q.phy "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/phyliptree_simple.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/phyliptree_simple.phy ] Executing @@ -1852,30 +1911,30 @@ storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/phyliptree_simple.phy -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas ] +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aarelaxedphylip_rana.phy +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aarelaxedphylip_rana.phy +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas ] Executing storing implied block: TAXA storing read block: DATA -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln -"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln" -[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln ] +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aafasta_twoprot.fas +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas" +[Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas ] Executing storing read block: TAXA storing read block: CHARACTERS -../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln +../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aafasta_twoprot.fas "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot.aln" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot.aln ] Executing @@ -1888,6 +1947,18 @@ storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot.aln +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidIn/aaaln_twoprot_undec.aln +"/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln" +[Reading /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/example/normalizer/NEXUSnormalizer succeeded for /build/libncl-2.1.21+git20190531.feceb81/test/ExternalValidOut/aaaln_twoprot_undec.aln /usr/bin/python3 ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn "/build/libncl-2.1.21+git20190531.feceb81/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/libncl-2.1.21+git20190531.feceb81/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy" [Reading /build/libncl-2.1.21+git20190531.feceb81/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy ] @@ -1981,8 +2052,8 @@ Making install in ncl make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' - /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf' - /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf' + /bin/sh ../libtool --mode=install /usr/bin/install -c libncl.la '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.so.2.0.0 libtool: install: (cd /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/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; }; }) @@ -1991,7 +2062,7 @@ libtool: install: chmod 644 /build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/libncl.a libtool: install: ranlib /build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/debian/tmp/usr/include/ncl' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/debian/tmp/usr/include/ncl' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81/ncl' @@ -2007,8 +2078,8 @@ Making install in check-taxo-nodes make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/check-taxo-nodes' - /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/debian/tmp/usr/bin/checktaxonnodes make[4]: Nothing to be done for 'install-data-am'. @@ -2024,8 +2095,8 @@ Making install in find-unsupported-edges make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/find-unsupported-edges' - /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/debian/tmp/usr/bin/findunsupportededges make[4]: Nothing to be done for 'install-data-am'. @@ -2055,8 +2126,8 @@ Making install in normalizer make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/normalizer' - /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/debian/tmp/usr/bin/NEXUSnormalizer libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' @@ -2069,8 +2140,8 @@ Making install in ot-subtree make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-subtree' - /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/debian/tmp/usr/bin/otsubtree make[4]: Nothing to be done for 'install-data-am'. @@ -2079,8 +2150,8 @@ Making install in ot-tree-inspect make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/ot-tree-inspect' - /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/debian/tmp/usr/bin/otTreeInspect make[4]: Nothing to be done for 'install-data-am'. @@ -2089,8 +2160,8 @@ Making install in outdeg1count make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' make[4]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81/example/outdeg1count' - /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/libncl-2.1.21+git20190531.feceb81/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+git20190531.feceb81/debian/tmp/usr/bin/outdeg1count make[4]: Nothing to be done for 'install-data-am'. @@ -2155,7 +2226,7 @@ make[2]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' make[3]: Entering directory '/build/libncl-2.1.21+git20190531.feceb81' make[3]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' + /usr/bin/mkdir -p '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 nclv2.1.pc '/build/libncl-2.1.21+git20190531.feceb81/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' make[3]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' make[2]: Leaving directory '/build/libncl-2.1.21+git20190531.feceb81' @@ -2199,23 +2270,23 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -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/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/outdeg1count 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/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/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/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/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/NCLconverter 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/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 dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libncl-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20190531.feceb81-3_armhf.deb'. -dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20190531.feceb81-3_armhf.deb'. dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20190531.feceb81-3_armhf.deb'. +dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20190531.feceb81-3_armhf.deb'. +dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20190531.feceb81-3_armhf.deb'. dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20190531.feceb81-3_armhf.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20190531.feceb81-3_armhf.deb'. dpkg-genbuildinfo --build=binary @@ -2225,12 +2296,14 @@ 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/18094/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18094/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/6296 and its subdirectories -I: Current time: Wed Aug 11 08:12:10 -12 2021 -I: pbuilder-time-stamp: 1628712730 +I: removing directory /srv/workspace/pbuilder/18094 and its subdirectories +I: Current time: Thu Aug 12 10:32:01 +14 2021 +I: pbuilder-time-stamp: 1628713921