I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 11 15:25:13 +14 2025 I: pbuilder-time-stamp: 1749605113 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libncl_2.1.21+git20210811.b1213a7-5.dsc] I: copying [./libncl_2.1.21+git20210811.b1213a7.orig.tar.xz] I: copying [./libncl_2.1.21+git20210811.b1213a7-5.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Aug 14 13:39:36 2023 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libncl_2.1.21+git20210811.b1213a7-5.dsc: no acceptable signature found dpkg-source: info: extracting libncl in libncl-2.1.21+git20210811.b1213a7 dpkg-source: info: unpacking libncl_2.1.21+git20210811.b1213a7.orig.tar.xz dpkg-source: info: unpacking libncl_2.1.21+git20210811.b1213a7-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_rpath_issue.patch dpkg-source: info: applying set_soname_version.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying python3.11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/986371/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 11 01:25 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/986371/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/986371/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=f87c2d5be7de4f1ea0aa42c70cde1152 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=986371 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lofBnhdY/pbuilderrc_H8t7 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lofBnhdY/b2 --logfile b2/build.log libncl_2.1.21+git20210811.b1213a7-5.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 10 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/986371/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19698 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 24.8 MB of archives. After unpacking 98.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 d-shlibs all 0.106 [10.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Fetched 24.8 MB in 2s (13.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19698 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20014 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21006 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../16-d-shlibs_0.106_all.deb ... Unpacking d-shlibs (0.106) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../24-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../26-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jun 11 01:26:14 UTC 2025. Universal Time is now: Wed Jun 11 01:26:14 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up d-shlibs (0.106) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... 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Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/986371/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/986371/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libncl_2.1.21+git20210811.b1213a7-5_source.changes dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20210811.b1213a7-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' dh_clean find . -name ".roundTripNCL*" -delete make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead dh_autoreconf libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'. libtoolize: copying file 'config/libtool.m4' libtoolize: copying file 'config/ltoptions.m4' libtoolize: copying file 'config/ltsugar.m4' libtoolize: copying file 'config/ltversion.m4' libtoolize: copying file 'config/lt~obsolete.m4' configure.ac:28: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:28: You should run autoupdate. config/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:28: the top level configure.ac:42: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:42: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... config/ax_cxx_flags.m4:5: AX_CXXFLAGS is expanded from... configure.ac:42: the top level configure.ac:124: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:124: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:124: the top level configure.ac:155: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:155: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:155: the top level configure.ac:167: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:167: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:167: the top level configure.ac:28: installing 'config/compile' configure.ac:21: installing 'config/missing' example/basiccmdline/Makefile.am: installing 'config/depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' dh_auto_configure -- --with-constfuncs=yes ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-constfuncs=yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /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 checking the name lister (/usr/bin/nm -B) interface... 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(cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C++ compiler works... yes checking for egrep... (cached) /usr/bin/grep -E checking for float.h... yes checking for stdlib.h... (cached) yes checking for _Bool... no checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking whether struct tm is in sys/time.h or time.h... time.h checking for sys/time.h... yes checking for alarm... yes checking for working mktime... yes checking for working strtod... yes checking for memmove... yes checking for strchr... yes checking for strtol... yes checking for python3... /usr/bin/python3 checking python3 module: subprocess... yes checking whether make sets $(MAKE)... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating example/Makefile config.status: creating example/basiccmdline/Makefile config.status: creating example/check-taxo-nodes/Makefile config.status: creating example/compressor/Makefile config.status: creating example/find-unsupported-edges/Makefile config.status: creating example/gapcode/Makefile config.status: creating example/ot-subtree/Makefile config.status: creating example/ot-tree-inspect/Makefile config.status: creating example/nclsimplest/Makefile config.status: creating example/ncltest/Makefile config.status: creating example/normalizer/Makefile config.status: creating example/patristic/Makefile config.status: creating example/phylobaseinterface/Makefile config.status: creating example/polytomy-count/Makefile config.status: creating example/outdeg1count/Makefile config.status: creating example/splitsinfile/Makefile config.status: creating example/subsetter/Makefile config.status: creating example/translate/Makefile config.status: creating ncl/Makefile config.status: creating test/Makefile config.status: creating nclv2.1.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make all-recursive make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' Making all in ncl make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. 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-fcf-protection -O3 -ffast-math -c nxsblock.cpp -fPIC -DPIC -o .libs/nxsblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsassumptionsblock.cpp -fPIC -DPIC -o .libs/nxsassumptionsblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxscxxdiscretematrix.cpp -fPIC -DPIC -o .libs/nxscxxdiscretematrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsmultiformat.cpp -fPIC -DPIC -o .libs/nxsmultiformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxstoken.cpp -fPIC -DPIC -o .libs/nxstoken.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from nxscharactersblock.cpp:26: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from nxscharactersblock.cpp:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxstoken.h:23, from ../ncl/nxssetreader.h:23, from nxssetreader.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from ../ncl/nxssetreader.h:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxstreesblock.h:25, from nxstreesblock.cpp:23: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from nxstreesblock.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxstaxaassociationblock.h:23, from nxstaxaassociationblock.cpp:25: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from nxstaxaassociationblock.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from nxstaxablock.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../ncl/nxsdefs.h:22, from ../ncl/nxstaxablock.h:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from nxsstring.cpp:25: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../ncl/nxsdefs.h:22, from nxsstring.cpp:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxstoken.h:23, from nxstoken.cpp:22: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from nxstoken.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from nxsexception.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/functional:49, from ../ncl/nxsstring.h:26: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from ../ncl/nxsdatablock.h:23, from nxsdatablock.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from ../ncl/nxscharactersblock.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from ../ncl/nxscxxdiscretematrix.h:28, from nxscxxdiscretematrix.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/streambuf:43, from /usr/include/c++/13/bits/streambuf_iterator.h:35, from /usr/include/c++/13/iterator:66, from nxscxxdiscretematrix.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from nxsblock.cpp:21: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../ncl/nxsdefs.h:22, from nxsblock.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, from ../ncl/nxsmultiformat.h:25, from nxsmultiformat.cpp:50: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from nxsmultiformat.cpp:48: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxsunalignedblock.h:24, from nxsunalignedblock.cpp:21: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../ncl/nxsdefs.h:22, from ../ncl/nxsunalignedblock.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsreader.h:24, from nxsreader.cpp:26: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from nxsreader.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxsdistancesblock.h:24, from nxsdistancesblock.cpp:23: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from nxsdistancesblock.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, from nxspublicblocks.cpp:24: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from nxspublicblocks.cpp:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxsassumptionsblock.h:26, from nxsassumptionsblock.cpp:22: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from nxsassumptionsblock.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxstaxaassociationblock.cpp -o nxstaxaassociationblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -version-info 2:0:0 -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/x86_64-linux-gnu nxsassumptionsblock.lo nxsblock.lo nxscharactersblock.lo nxscxxdiscretematrix.lo nxsdatablock.lo nxsdistancesblock.lo nxsexception.lo nxsmultiformat.lo nxspublicblocks.lo nxsreader.lo nxssetreader.lo nxsstring.lo nxstaxablock.lo nxstaxaassociationblock.lo nxstoken.lo nxstreesblock.lo nxsunalignedblock.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/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/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -O3 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libncl.so.2" && ln -s "libncl.so.2.0.0" "libncl.so.2") libtool: link: (cd ".libs" && rm -f "libncl.so" && ln -s "libncl.so.2.0.0" "libncl.so") libtool: link: ar cr .libs/libncl.a nxsassumptionsblock.o nxsblock.o nxscharactersblock.o nxscxxdiscretematrix.o nxsdatablock.o nxsdistancesblock.o nxsexception.o nxsmultiformat.o nxspublicblocks.o nxsreader.o nxssetreader.o nxsstring.o nxstaxablock.o nxstaxaassociationblock.o nxstoken.o nxstreesblock.o nxsunalignedblock.o libtool: link: ranlib .libs/libncl.a libtool: link: ( cd ".libs" && rm -f "libncl.la" && ln -s "../libncl.la" "libncl.la" ) make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' Making all in example make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' Making all in basiccmdline make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o basiccmdline.o basiccmdline.cpp In file included from ../../ncl/ncl.h:79, from basiccmdline.cpp:20: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' Making all in check-taxo-nodes make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o checktaxonnodes-checktaxonnodes.o `test -f 'checktaxonnodes.cpp' || echo './'`checktaxonnodes.cpp In file included from ../../ncl/ncl.h:79, from checktaxonnodes.cpp:20: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' Making all in compressor make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUSCharacterCompressor-compressor.o `test -f 'compressor.cpp' || echo './'`compressor.cpp In file included from ../../ncl/nxsexception.h:23, from ../../ncl/nxsblock.h:24, from ../../ncl/nxstaxablock.h:23, from ../../ncl/nxscharactersblock.h:29, from ../../ncl/nxscxxdiscretematrix.h:28, from compressor.cpp:4: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from compressor.cpp:1: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' Making all in find-unsupported-edges make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o findunsupportededges-findunsupportededges.o `test -f 'findunsupportededges.cpp' || echo './'`findunsupportededges.cpp In file included from ../../ncl/ncl.h:79, from findunsupportededges.cpp:20: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' Making all in gapcode make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUSgapcode-gapcode.o `test -f 'gapcode.cpp' || echo './'`gapcode.cpp In file included from ../../ncl/ncl.h:79, from gapcode.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' Making all in nclsimplest make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' g++ -DHAVE_CONFIG_H -I. -I../.. -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o nclsimplest.o nclsimplest.cpp In file included from ../../ncl/ncl.h:79, from nclsimplest.cpp:1: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' Making all in ncltest make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o ncltest.o ncltest.cpp In file included from ../../ncl/ncl.h:79, from ncltest.cpp:20: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' Making all in normalizer make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o normalizer.o normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_VALIDATE_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUSvalidator-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NCLconverter-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEX_us2ml-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DMULTIFILE_NEXUS_READER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from converter.cpp:48: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from us2ml.cpp:22: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from us2ml.cpp:22: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' Making all in ot-subtree make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o otsubtree-otsubtree.o `test -f 'otsubtree.cpp' || echo './'`otsubtree.cpp In file included from ../../ncl/ncl.h:79, from otsubtree.cpp:20: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' Making all in ot-tree-inspect make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o otTreeInspect-ot_tree_inspect.o `test -f 'ot_tree_inspect.cpp' || echo './'`ot_tree_inspect.cpp In file included from ../../ncl/ncl.h:79, from ot_tree_inspect.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' Making all in outdeg1count make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o outdeg1count-outdeg1count.o `test -f 'outdeg1count.cpp' || echo './'`outdeg1count.cpp In file included from ../../ncl/ncl.h:79, from outdeg1count.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' Making all in patristic make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o patristic.o patristic.cpp In file included from ../../ncl/ncl.h:79, from patristic.cpp:33: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' Making all in phylobaseinterface make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NCLInterface.o NCLInterface.cpp In file included from ../../ncl/ncl.h:79, from NCLInterface.cpp:24: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' Making all in polytomy-count make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o polytomycount-polytomy_count.o `test -f 'polytomy_count.cpp' || echo './'`polytomy_count.cpp In file included from ../../ncl/ncl.h:79, from polytomy_count.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' Making all in splitsinfile make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUStosplits-splitsinfile.o `test -f 'splitsinfile.cpp' || echo './'`splitsinfile.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUStosplits-splitsstructs.o `test -f 'splitsstructs.cpp' || echo './'`splitsstructs.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o splitsinfile.o splitsinfile.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o splitsstructs.o splitsstructs.cpp In file included from ../../ncl/nxsexception.h:23, from ../../ncl/nxsblock.h:24, from ../../ncl/nxstaxablock.h:23, from ../../ncl/nxstreesblock.h:25, from splitsstructs.h:9, from splitsstructs.cpp:1: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from splitsstructs.h:3: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from splitsinfile.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/nxsexception.h:23, from ../../ncl/nxsblock.h:24, from ../../ncl/nxstaxablock.h:23, from ../../ncl/nxstreesblock.h:25, from splitsstructs.h:9, from splitsstructs.cpp:1: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from splitsstructs.h:3: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from splitsinfile.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' Making all in subsetter make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUSsubsetter-subsetter.o `test -f 'subsetter.cpp' || echo './'`subsetter.cpp In file included from ../../ncl/nxsexception.h:23, from ../../ncl/nxsblock.h:24, from ../../ncl/nxspublicblocks.h:24, from ../../ncl/nxsmultiformat.h:25, from subsetter.cpp:4: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from subsetter.cpp:1: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' Making all in translate make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -c -o NEXUStranslate-translateNuc.o `test -f 'translateNuc.cpp' || echo './'`translateNuc.cpp In file included from ../../ncl/ncl.h:79, from translateNuc.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -ffast-math -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' Making all in test make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test' make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' dh_auto_test make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' Making check in ncl make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' Making check in example make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' Making check in basiccmdline make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' Making check in check-taxo-nodes make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' Making check in compressor make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' Making check in find-unsupported-edges make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' Making check in gapcode make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' Making check in nclsimplest make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' Making check in ncltest make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' make check-local make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/ncltest/ncltest ../../test/OldValidIn ../../test/OldValidOut "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest/ncltest" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/OldValidIn/m.nex" [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest/ncltest succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/OldValidIn/m.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest/ncltest" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/OldValidOut/m.nex" [Reading -s2 ] [Reading -s2 ] storing read block: TAXA storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest/ncltest succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/OldValidOut/m.nex make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' Making check in normalizer make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' make check-local make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/characters.nex ../../test/data "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/characters.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/characters.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/characters.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/characters.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/characters.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/characters.nex /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer/NEXUSnormalizer ../../data/sample.tre ../../test/data "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/sample.tre" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/sample.tre ] Executing storing read block: PAUP storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/data/sample.tre "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/sample.tre" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/sample.tre ] Executing storing read block: PAUP storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/data/sample.tre /usr/bin/python3 ../../test/roundTripNCLTest.py ../../example/normalizer//NEXUSnormalizer ../../test/NTSValidIn ../../test/NTSValidOut "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 189) storing read block: TAXA Warning: Skipping command: blockid at line 27, column (approximately) 11 (file position 388) storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS Warning: Skipping unknown LINK subcommand: characters at line 61, column (approximately) 38 (file position 1551) storing read block: TREES Warning: Skipping unknown LINK subcommand: characters at line 71, column (approximately) 38 (file position 1745) storing read block: TREES storing implied block: ASSUMPTIONS storing implied block: ASSUMPTIONS storing read block: ASSUMPTIONS Warning: A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s). at line 90, column (approximately) 42 (file position 2360) storing read block: ASSUMPTIONS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/linktest.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 168) storing read block: TAXA Warning: Skipping command: blockid at line 12, column (approximately) 13 (file position 341) storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: TREES storing read block: TREES storing read block: SETS storing read block: SETS storing read block: SETS Warning: A TaxSet with the name o has already been encountered. The later definition will preempt the earlier definition(s). at line 84, column (approximately) 20 (file position 2384) storing read block: SETS storing read block: SETS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/linktest.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/m.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/m.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/m.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/m.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/m.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: SETS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/m.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/mdata.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: SETS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/mdata.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/avian_ovomucoids.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/avian_ovomucoids.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-dos.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-dos.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-unix.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-unix.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-rake.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-rake.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: CODONS Warning: An * is ignored in a CHARSET command at line 67, column (approximately) 46 (file position 929) Warning: An * is ignored in a CHARSET command at line 68, column (approximately) 42 (file position 968) storing read block: ASSUMPTIONS storing read block: ASSUMPTIONS storing read block: MESQUITECHARMODELS storing read block: MESQUITE ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-rake.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-rake.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-rake.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: CODONS storing read block: SETS storing read block: ASSUMPTIONS storing read block: MESQUITECHARMODELS storing read block: MESQUITE ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-rake.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 3, column (approximately) 7 (file position 26) storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock-quotes.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock-quotes.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex ] Executing storing read block: TAXA storing read block: DISTANCES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/distances.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/distances.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/distances.nex ] Executing storing read block: TAXA storing read block: DISTANCES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/distances.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/cynmix.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/cynmix.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/cynmix.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/cynmix.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/bglobin.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/bglobin.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/adh.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/adh.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/adh.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/adh.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/adh.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/adh.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 3, column (approximately) 13 (file position 32) storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/notaxablock.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/notaxablock.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 3, column (approximately) 10 (file position 26) storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/treeswithouttaxa.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/treeswithouttaxa.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/unaligned.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex ] Executing storing read block: TAXA storing read block: UNALIGNED ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/unaligned.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mixed-line-endings.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mixed-line-endings.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/characters.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/characters.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/paup_characters.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 188) storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/paup_characters.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/protein.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/protein.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/anolis.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/anolis.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/kim.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/kim.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: CODONS Warning: An * is ignored in a CHARSET command at line 67, column (approximately) 46 (file position 1014) Warning: An * is ignored in a CHARSET command at line 68, column (approximately) 42 (file position 1053) storing read block: ASSUMPTIONS storing read block: ASSUMPTIONS storing read block: MESQUITECHARMODELS storing read block: MESQUITE ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/nhxtree.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: CODONS storing read block: SETS storing read block: ASSUMPTIONS storing read block: MESQUITECHARMODELS storing read block: MESQUITE ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/nhxtree.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/t.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/t.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/replicase.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/replicase.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/basic-bush-mac.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/basic-bush-mac.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/charsets.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/charsets.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS storing read block: SETS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/charsets.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/charsets.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/charsets.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS storing read block: SETS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/charsets.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex ] Executing Warning: Skipping command: blockid at line 13, column (approximately) 11 (file position 176) storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: SETS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/partitions.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex ] Executing Warning: Skipping command: blockid at line 6, column (approximately) 13 (file position 183) storing read block: TAXA storing read block: CHARACTERS storing read block: TREES storing read block: SETS storing read block: ASSUMPTIONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/partitions.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex ] Executing storing read block: TAXA storing read block: TAXA storing read block: TAXAASSOCIATION ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/associates.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex ] Executing storing read block: TAXA storing read block: TAXA storing read block: TAXAASSOCIATION ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/associates.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: ASSUMPTIONS storing read block: MACCLADE ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/dzmissing_bug.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex ] Executing storing read block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS storing read block: MACCLADE ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/dzmissing_bug.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/primates.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/primates.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidIn/parens_intree.tre "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/parens_intree.tre" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/parens_intree.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/NTSValidOut/parens_intree.tre /usr/bin/python3 ../../test/roundTripNCLTest.py -x ../../example/normalizer/NEXUSnormalizer ../../test/funkyValidIn ../../test/funkyValidOut "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidIn/choke.tre" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidIn/choke.tre ] Executing Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 5, column (approximately) 6 (file position 74) storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidIn/choke.tre "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-x" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidOut/choke.tre" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidOut/choke.tre ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/funkyValidOut/choke.tre /usr/bin/python3 ../../test/roundTripNCLTest.py -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalValidIn ../../test/ExternalValidOut "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_rana.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_rana.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylipinterleaved" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aarelaxedphylip_rana.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aarelaxedphylip_rana.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fphyliptree" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/phyliptree_simple.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/phyliptree_simple.phy ] Executing storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/phyliptree_simple.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/phyliptree_simple.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/phyliptree_simple.phy ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/phyliptree_simple.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-frelaxedphyliptree" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/relaxedphyliptree_q.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/relaxedphyliptree_q.phy ] Executing storing implied block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/relaxedphyliptree_q.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/relaxedphyliptree_q.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/relaxedphyliptree_q.phy ] Executing storing read block: TAXA storing read block: TREES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/relaxedphyliptree_q.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylip_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/dnarelaxedphylip_brana.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/dnarelaxedphylip_brana.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faafasta" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aafasta_twoprot.fas "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aafasta_twoprot.fas "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot_undec.aln "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot_undec.aln "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaaln" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot.aln" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot.aln ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaaln_twoprot.aln "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot.aln" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot.aln ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaaln_twoprot.aln /usr/bin/python3 ../../test/roundTripNCLTest.py -i -e ../../example/normalizer/NEXUSnormalizer ../../test/ExternalInvalidIn "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-fdnarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/dnarelaxedphylip_rana.phy ] Executing Error: Illegal state code "q" found when reading site 2 for taxon grylioMVZ175945 at line 12, column (approximately) 28 (and file position 20065) "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faarelaxedphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/aarelaxedphylip_rana.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalInvalidIn/aarelaxedphylip_rana.phy ] Executing Error: Sequence longer than 1976 found for taxon temporariaDMH84R1. The character "o" was found, and will be ignored. If the file position of this error corresponds to sequences for the next taxon in the matrix, then that is an indication that the sequences for taxon temporariaDMH84R1 are too short. at line 3, column (approximately) 2 (and file position 2011) /usr/bin/python3 ../../test/roundTripNCLTest.py -a ../../example/normalizer/NEXUSnormalizer /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/.debhelper/generated/_source/home/.ncl_round_triprc does not exist. Test stepped skipped. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' Making check in ot-subtree make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' Making check in ot-tree-inspect make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' Making check in outdeg1count make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' Making check in patristic make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' Making check in phylobaseinterface make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' Making check in polytomy-count make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' Making check in splitsinfile make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' Making check in subsetter make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' Making check in translate make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make check-local make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' /usr/bin/python3 ../../test/roundTripNCLTest.py -o ../../example/translate/NEXUStranslate ../../test/TranslateIn ../../test/TranslateOut "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: CODONS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobinoof.nex "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: MRBAYES ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate/NEXUStranslate succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/TranslateIn/bglobin.nex make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' Making check in test make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test' make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libncl-2.1.21\+git20210811.b1213a7/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' Making install in ncl make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libncl.la '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libncl.so.2.0.0 /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libncl.so.2.0.0 libncl.so.2 || { rm -f libncl.so.2 && ln -s libncl.so.2.0.0 libncl.so.2; }; }) libtool: install: (cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libncl.so.2.0.0 libncl.so || { rm -f libncl.so && ln -s libncl.so.2.0.0 libncl.so; }; }) libtool: install: /usr/bin/install -c .libs/libncl.lai /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.la libtool: install: /usr/bin/install -c .libs/libncl.a /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.a libtool: install: chmod 644 /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.a libtool: install: ranlib /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/include/ncl' /usr/bin/install -c -m 644 ncl.h nxsallocatematrix.h nxsassumptionsblock.h nxsblock.cpp nxsblock.h nxscharactersblock.h nxscdiscretematrix.h nxscxxdiscretematrix.h nxsdatablock.h nxsdefs.h nxsdiscretedatum.h nxsdistancedatum.h nxsdistancesblock.h nxsexception.h nxsmultiformat.h nxspublicblocks.h nxsreader.h nxssetreader.h nxsstring.h nxstaxablock.h nxstaxaassociationblock.h nxstoken.h nxstreesblock.h nxsunalignedblock.h nxsutilcopy.h '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/include/ncl' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' Making install in example make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' Making install in basiccmdline make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' Making install in check-taxo-nodes make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/checktaxonnodes /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/checktaxonnodes make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' Making install in compressor make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' Making install in find-unsupported-edges make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/findunsupportededges /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/findunsupportededges make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' Making install in gapcode make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' Making install in nclsimplest make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' Making install in ncltest make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' Making install in normalizer make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSnormalizer /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/NEXUSnormalizer libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NEXUSvalidator /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/NEXUSvalidator libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/NCLconverter /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/NCLconverter make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' Making install in ot-subtree make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/otsubtree /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/otsubtree make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' Making install in ot-tree-inspect make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/otTreeInspect /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/otTreeInspect make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' Making install in outdeg1count make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/outdeg1count /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin/outdeg1count make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' Making install in patristic make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' Making install in phylobaseinterface make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' Making install in polytomy-count make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' Making install in splitsinfile make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' Making install in subsetter make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' Making install in translate make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' Making install in test make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test' make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test' make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test' make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 nclv2.1.pc '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make[3]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[2]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/ncl/*.h" usr/include/ncl \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/x86_64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/libncl.so Library package automatic movement utility set -e install -d -m 755 debian/libncl-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libncl2/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libncl.a debian/libncl-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libncl.la debian/libncl-dev/usr/lib/x86_64-linux-gnu || true mv debian/tmp/usr/lib/x86_64-linux-gnu/libncl.so debian/libncl-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/x86_64-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/x86_64-linux-gnu PKGDEV=libncl-dev PKGSHL=libncl2 install -d -m 755 debian/libncl-dev/usr/include/ncl mv debian/tmp/usr/include/ncl/*.h debian/libncl-dev/usr/include/ncl install -d -m 755 debian/libncl-dev/usr/lib/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libncl-dev/usr/lib/x86_64-linux-gnu/pkgconfig rm -f debian/tmp/usr/include/ncl/nxsblock.cpp make[1]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libncl-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20210811.b1213a7-5_amd64.deb'. dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20210811.b1213a7-5_amd64.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20210811.b1213a7-5_amd64.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20210811.b1213a7-5_amd64.deb'. dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libncl_2.1.21+git20210811.b1213a7-5_amd64.buildinfo dpkg-genchanges --build=binary -O../libncl_2.1.21+git20210811.b1213a7-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/986371/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/986371/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/986371 and its subdirectories I: Current time: Wed Jun 11 15:34:24 +14 2025 I: pbuilder-time-stamp: 1749605664